Is ITGA5 p.Phe782= (c.2346T>C) pathogenic?

ITGA5 p.Phe782= (c.2346T>C) is classified Benign in ITGA5 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-11-12). Common (popmax 12.1%, afr) — too common for a highly-penetrant pathogenic allele.

ITGA5 p.Phe782=

Q: How common is ITGA5 p.Phe782= (c.2346T>C) in the general population?

ITGA5 p.Phe782= (c.2346T>C) is common (popmax 12.1%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2346T>C · rs73322228 · VCV1243290

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 12.1%, 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 8.6	GERP 1, phastCons 1
Overall
CADD	13.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 12.1% African / African-American · 9,054/74,958 alleles

Filtering AF 11.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 11.8%

Overall 1.92% 31,042/1,614,046 alleles · common exomes 24,527/1,461,874 · genomes 6,515/152,172 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	12.1%	8
South Asian	7.63%	13
Remaining individualsnot grpmax-eligible	2.23%	45
Ashkenazi Jewishnot grpmax-eligible	2.04%	49
Finnishnot grpmax-eligible	1.4%	71
Middle Eastern	1.25%	80
Admixed American	1.09%	92
European (non-Finnish)	0.943%	106
East Asian	0.624%	160

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: ITGA5
Protein: p.Phe782=
Coding: c.2346T>C
MANE Select: NM_002205
dbSNP: rs73322228
Type: single nucleotide variant
Location: chr12:54401626 (GRCh38)

Full ITGA5 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/itga5-p-phe782 (accessed [today's date]).

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