Is AHSG p.Ala170= (c.510C>T) pathogenic?

AHSG p.Ala170= (c.510C>T) is classified Benign/Likely benign in AHSG (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-09-23). Rare (popmax 0.703%, afr).

How common is AHSG p.Ala170= (c.510C>T) in the general population?

AHSG p.Ala170= (c.510C>T) is rare (popmax 0.703%, afr) (gnomAD).

AHSG p.Ala170=

c.510C>T · rs78152999 · VCV790549

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.703%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Overall
CADD	7.284	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.703% African / African-American · 528/75,054 alleles

Filtering AF 0.654% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.634%

Overall 0.0377% 608/1,614,226 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.703%	142
Middle Eastern	0.132%	758
Remaining individualsnot grpmax-eligible	0.0672%	1,488
Admixed American	0.0383%	2,610
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608
South Asian	0.0011%	91,086
European (non-Finnish)	0.000424%	236,009

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: AHSG
Protein: p.Ala170=
Coding: c.510C>T
MANE Select: NM_001622
dbSNP: rs78152999
Type: single nucleotide variant
Location: chr3:186617287 (GRCh38)
Gene constraint: LOEUF 1.042 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.59
Residue 170: a disulfide bond; the cystatin fetuin-a-type 2 domain

Full AHSG gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AHSG p.Ala170Thr Uncertain significance ★ ⚠ same residue
AHSG p.Val342Met Uncertain significance ★★ ⚠ same type
AHSG p.Arg317Cys Benign ★★ same type
AHSG p.Met248Thr Benign ★★ same type
AHSG p.Ser256Thr Benign ★★ same type
AHSG p.Thr270= Benign ★★ same type
AHSG p.Val142Leu Benign ★★ same type
AHSG p.Arg317His Likely pathogenic ★ ⚠ 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/ahsg-p-ala170 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown