# NM_024603.4(BEND5):c.24G>A (p.Leu8=)

https://sugi.bio/variant/bend5-p-leu8

## Summary

**BEND5 p.Leu8= (c.24G>A)** is classified **Likely benign** in BEND5 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-26). Very rare (popmax 0.00741%, sas).

**At a glance:** Likely benign · review: Single submitter · 1 submitter · very rare (popmax 0.00741%, sas)

## For patients & families {#patients}

This is a change in the BEND5 gene that is classified as likely benign — not considered disease-causing, 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 | [BEND5](https://sugi.bio/atlas/gene/BEND5/) |
| Protein change (HGVS p.) | p.Leu8= |
| Coding change (HGVS c.) | c.24G>A |
| MANE Select transcript | [NM_032785](https://www.ncbi.nlm.nih.gov/nuccore/NM_032785) (variant reported on NM_024603) |
| Variant type | single nucleotide variant |
| Location | chr1:48776808-48776808 (GRCh38) |
| ClinVar | [VCV3480444](https://www.ncbi.nlm.nih.gov/clinvar/variation/3480444/) |

**All HGVS expressions:** `NC_000001.10:g.49242480C>T`, `NC_000001.11:g.48776808C>T`, `NG_053063.1:g.6796G>A`, `NM_001302082.2:c.-566G>A`, `NM_001323573.2:c.670+90383G>A`, `NM_001323574.2:c.670+90383G>A`, `NM_001323575.2:c.634+90383G>A`, `NM_001349793.2:c.-350G>A`, `NM_001349794.2:c.-763G>A`, `NM_001349795.2:c.-506G>A`, `NM_024603.4:c.24G>A`, `NM_032785.4:c.634+90383G>A`, `NR_146232.2:n.84G>A`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 5.575, GERP 1.69, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 15.54**. 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.*
- SpliceAI: **not looked up on this page** — it was served without the gene's SpliceAI index, so no lookup was made. This is a gap in this page, not in the data, and says nothing about whether a splicing effect is predicted.
- Pangolin: Δ**0.29** (gain), gain 0.29 / loss 0.00. An independent predictor to SpliceAI — a different model trained on different data. *Descriptive; ClinGen's SVI calibration covers SpliceAI, not Pangolin, so no ACMG code is assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.00741%** (sas) · FAF95 0.00316% · FAF99 0.00214% · 6/80,984 in the highest group · 8/1,370,262 alleles overall — very rare (popmax 0.00741%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 0.00741% | 13,497 |
| Remaining individuals (not grpmax-eligible) | 0.0017% | 58,866 |
| African / African-American | 0.00144% | 69,354 |

*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.*

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2024-09-26.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-09-26 |

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

### 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 3480444). 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.*