Is DHX32 p.Ala510= (c.1530A>G) pathogenic?

DHX32 p.Ala510= (c.1530A>G) is classified Benign in DHX32 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-04). Common (popmax 58.1%, afr) — too common for a highly-penetrant pathogenic allele.

DHX32 p.Ala510=

Q: How common is DHX32 p.Ala510= (c.1530A>G) in the general population?

DHX32 p.Ala510= (c.1530A>G) is common (popmax 58.1%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1530A>G · rs3208565 · VCV1599286

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 58.1%, afr) — too common for a highly-penetrant pathogenic allele

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 -0.98	GERP -3.5
Overall
CADD	0.665	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 58.1% African / African-American · 43,371/74,684 alleles

Filtering AF 57.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 57.4%

Overall 46.4% 746,304/1,610,018 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	58.1%	2
European (non-Finnish)	47.6%	2
Amishnot grpmax-eligible	47.6%	2
South Asian	45.4%	2
Remaining individualsnot grpmax-eligible	44.9%	2
Finnishnot grpmax-eligible	43.2%	2
Ashkenazi Jewishnot grpmax-eligible	41%	2
Middle Eastern	33.7%	3
East Asian	32.2%	3
Admixed American	28%	4

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: DHX32
Protein: p.Ala510=
Coding: c.1530A>G
MANE Select: NM_018180
dbSNP: rs3208565
Type: single nucleotide variant
Location: chr10:125841756 (GRCh38)
Gene constraint: LOEUF 0.919 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.34

Full DHX32 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DHX32 p.Ala251Val Uncertain significance ★★ ⚠ same type
DHX32 p.Ala93Thr Uncertain significance ★★ ⚠ same type
DHX32 p.Arg129Gln Uncertain significance ★★ ⚠ same type
DHX32 p.Arg261Cys Uncertain significance ★★ ⚠ same type
DHX32 p.Arg261His Uncertain significance ★★ ⚠ same type
DHX32 p.Asn239Lys Uncertain significance ★★ ⚠ same type
DHX32 p.Asn297His Uncertain significance ★★ ⚠ same type
DHX32 p.Asn297Ile Uncertain significance ★★ ⚠ 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/dhx32-p-ala510 (accessed [today's date]).

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