ABCA5 p.Ser885=
c.2655T>C · rs137864439 · VCV726893
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.09%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 7.116 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.09%
South Asian · 977/89,514 alleles
Filtering AF
1.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.01%
Overall
0.0696%
1,120/1,609,288 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.09% | 92 |
| Middle Eastern | 0.233% | 430 |
| Remaining individualsnot grpmax-eligible | 0.0867% | 1,154 |
| Admixed American | 0.017% | 5,891 |
| East Asian | 0.00669% | 14,949 |
| African / African-American | 0.00535% | 18,675 |
| European (non-Finnish) | 0.00484% | 20,679 |
| Finnishnot grpmax-eligible | 0.00156% | 63,952 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ABCA5
- Protein
- p.Ser885=
- Coding
- c.2655T>C
- MANE Select
- NM_172232
- dbSNP
- rs137864439
- Type
- single nucleotide variant
- Location
- chr17:69274068 (GRCh38)
- Gene constraint
- LOEUF 0.97 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.12
Similar variants
- ABCA5 p.Ser288Phe Uncertain significance ★★ ⚠ same type
- ABCA5 c.4765+3A>G Likely benign ★★ same type
- ABCA5 p.Asn190Ser Likely benign ★★ ⚠ same type
- ABCA5 p.Asn768Asp Benign ★★ same type
- ABCA5 p.Asp817Tyr Likely benign ★★ ⚠ same type
- ABCA5 p.Gly1159Arg Likely benign ★★ ⚠ same type
- ABCA5 p.Gly128= Benign/Likely benign ★★ same type
- ABCA5 p.Ile1173Val Likely benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/abca5-p-ser885 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown