# NM_033364.4(CFAP91):c.245A>G (p.His82Arg)

https://sugi.bio/variant/cfap91-p-his82arg

## Summary

**CFAP91 p.His82Arg (c.245A>G)** is classified **Uncertain significance** in CFAP91 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-01). AlphaMissense: likely benign (0.1202); Very rare (popmax 0.00225%, eas).

**At a glance:** Uncertain significance · review: Single submitter · rsID rs1182876976 · 1 submitter · AlphaMissense likely benign · very rare (popmax 0.00225%, eas)

## For patients & families {#patients}

This is a change in the CFAP91 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CFAP91](https://sugi.bio/atlas/gene/CFAP91/) |
| Protein change (HGVS p.) | p.His82Arg |
| Coding change (HGVS c.) | c.245A>G |
| MANE Select transcript | [NM_033364](https://www.ncbi.nlm.nih.gov/nuccore/NM_033364) |
| dbSNP | [rs1182876976](https://www.ncbi.nlm.nih.gov/snp/rs1182876976/) |
| Variant type | single nucleotide variant |
| Location | chr3:119707447-119707447 (GRCh38) |
| ClinVar | [VCV2492191](https://www.ncbi.nlm.nih.gov/clinvar/variation/2492191/) |

**All HGVS expressions:** `NC_000003.11:g.119426294A>G`, `NC_000003.12:g.119707447A>G`, `NM_001320316.2:c.185A>G`, `NM_001320317.2:c.59A>G`, `NM_001320318.2:c.-19-1144A>G`, `NM_033364.4:c.245A>G`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.1202)
- REVEL 0.104 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -6.165 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 8.028, GERP 0.763, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 19.59**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 1.02** across the covering region of the MANE Select transcript (119,703,099–119,751,094), spanning 47,995 bp. Chi-square p 0.55. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (A>T, Δ0.21 acceptor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.00225%** (eas) · FAF95 0.000186% · FAF99 0.000122% · 1/44,434 in the highest group · 9/1,586,030 alleles overall — very rare (popmax 0.00225%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.00225% | 44,434 |
| Admixed American | 0.00168% | 59,352 |
| South Asian | 0.00115% | 87,038 |
| European (non-Finnish) | 0.000517% | 193,548 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**CFAP91** population constraint: LOEUF 1.129, pLI 9.8021e-20, missense-Z 0.12954. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 75.20, 23% of residues very-high.

**1 experimental structure(s)** (PDB): [8J07](https://www.rcsb.org/structure/8J07).

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-03-01.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-03-01 |

**Reported phenotype names (ClinVar):** not specified, AllHighlyPenetrant.

## Similar variants {#similar}

Related CFAP91 variant pages (same residue, condition, or type): [CFAP91 c.359+1G>A](/variant/cfap91-c-359-plus-1g-a), [CFAP91 p.Gln545Ter](/variant/cfap91-p-gln545ter), [CFAP91 c.501-3T>C](/variant/cfap91-c-501-minus-3t-c), [CFAP91 p.Ala249Asp](/variant/cfap91-p-ala249asp), [CFAP91 p.Ala256Thr](/variant/cfap91-p-ala256thr), [CFAP91 p.Ala449Val](/variant/cfap91-p-ala449val), [CFAP91 p.Ala598Ser](/variant/cfap91-p-ala598ser), [CFAP91 p.Ala718Thr](/variant/cfap91-p-ala718thr).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 2492191). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*