Is STRN4 p.Val10= (c.30C>A) pathogenic?

STRN4 p.Val10= (c.30C>A) is classified Likely benign in STRN4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-02-26). Common (popmax 5.05%, afr) — too common for a highly-penetrant pathogenic allele.

STRN4 p.Val10=

Q: How common is STRN4 p.Val10= (c.30C>A) in the general population?

STRN4 p.Val10= (c.30C>A) is common (popmax 5.05%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.30C>A · rs569440158 · VCV781468

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 5.05%, afr) — too common for a highly-penetrant pathogenic allele

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.5	GERP -1.4, phastCons 1
Overall
CADD	7.213	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.05% African / African-American · 2,951/58,400 alleles

Filtering AF 4.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.84%

Overall 0.3% 3,184/1,060,528 alleles · common exomes 1,103/913,458 · genomes 2,081/147,070 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5.05%	20
Admixed American	0.456%	219
Remaining individualsnot grpmax-eligible	0.35%	286
Middle Eastern	0.214%	467
South Asian	0.022%	4,536
European (non-Finnish)	0.00216%	46,397

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: STRN4
Protein: p.Val10=
Coding: c.30C>A
MANE Select: NM_013403
dbSNP: rs569440158
Type: single nucleotide variant
Location: chr19:46746401 (GRCh38)

Full STRN4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/strn4-p-val10 (accessed [today's date]).

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