Is BIRC6 p.Arg1870= (c.5610A>G) pathogenic?

BIRC6 p.Arg1870= (c.5610A>G) is classified Likely benign in BIRC6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-11). Ultra-rare (popmax 0.0523%, nfe); Associated with BIRC6-related disorder.

What condition is associated with BIRC6 p.Arg1870= (c.5610A>G)?

BIRC6 p.Arg1870= (c.5610A>G) is associated with BIRC6-related disorder (ClinVar).

How common is BIRC6 p.Arg1870= (c.5610A>G) in the general population?

BIRC6 p.Arg1870= (c.5610A>G) is ultra-rare (popmax 0.0523%, nfe) (gnomAD).

BIRC6 p.Arg1870=

c.5610A>G · rs140684752 · VCV3039624

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0523%, nfe)

Conditions

BIRC6-related disorder

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 9.4	GERP 2.8, phastCons 1
Overall
CADD	11.98	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0523% European (non-Finnish) · 617/1,179,782 alleles

Filtering AF 0.0488% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0475%

Overall 0.0411% 663/1,613,612 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0523%	1,912
Remaining individualsnot grpmax-eligible	0.0304%	3,287
Admixed American	0.015%	6,665
African / African-American	0.0107%	9,366
Finnishnot grpmax-eligible	0.00781%	12,802
South Asian	0.00549%	18,202

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: BIRC6
Protein: p.Arg1870=
Coding: c.5610A>G
MANE Select: NM_016252
dbSNP: rs140684752
Type: single nucleotide variant
Location: chr2:32467941 (GRCh38)
Gene constraint: LOEUF 0.213 · pLI 1.00 (gnomAD)

Full BIRC6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BIRC6-related disorder

Similar variants

BIRC6 p.Gln853Arg Uncertain significance ★★ ⚠ same condition
BIRC6 p.Glu4506Asp Uncertain significance ★★ ⚠ same condition
BIRC6 p.Arg1075Gln Uncertain significance ★ ⚠ same condition
BIRC6 p.Asp386Glu Uncertain significance ★ same condition
BIRC6 p.Asp673His Uncertain significance ★ same condition
BIRC6 p.Ser1258Ala Uncertain significance ★ ⚠ same condition
BIRC6 p.Ser3427Phe Uncertain significance ★ same condition
BIRC6 p.Asp3819Tyr Uncertain significance same condition

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/birc6-p-arg1870 (accessed [today's date]).

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