Is BCAS3 p.Arg574= (c.1720A>C) pathogenic?

BCAS3 p.Arg574= (c.1720A>C) is classified Likely benign in BCAS3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-01). Rare (popmax 0.817%, nfe).

How common is BCAS3 p.Arg574= (c.1720A>C) in the general population?

BCAS3 p.Arg574= (c.1720A>C) is rare (popmax 0.817%, nfe) (gnomAD).

BCAS3 p.Arg574=

c.1720A>C · rs139961894 · VCV2647996

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.817%, nfe)

⚠ 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 6.7	GERP 1.9, phastCons 1
Overall
CADD	17.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.817% European (non-Finnish) · 9,638/1,179,354 alleles

Filtering AF 0.804% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.798%

Overall 0.689% 11,112/1,612,952 alleles · rare exomes 10,307/1,460,644 · genomes 805/152,308 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	1.09%	91
European (non-Finnish)grpmax	0.817%	122
Remaining individualsnot grpmax-eligible	0.629%	159
South Asian	0.186%	538
Admixed American	0.175%	571
Middle Eastern	0.132%	757
African / African-American	0.101%	987
Ashkenazi Jewishnot grpmax-eligible	0.071%	1,408
East Asian	0.00446%	22,403

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: BCAS3
Protein: p.Arg574=
Coding: c.1720A>C
MANE Select: NM_017679
dbSNP: rs139961894
Type: single nucleotide variant
Location: chr17:61034748 (GRCh38)

Full BCAS3 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/bcas3-p-arg574 (accessed [today's date]).

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