Is BCAS4 p.Asp5Asn (c.13G>A) pathogenic?

BCAS4 p.Asp5Asn (c.13G>A) is classified Likely benign in BCAS4 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-07). AlphaMissense: likely benign (0.1485); Very rare (popmax 0.000532%, nfe).

How common is BCAS4 p.Asp5Asn (c.13G>A) in the general population?

BCAS4 p.Asp5Asn (c.13G>A) is very rare (popmax 0.000532%, nfe) (gnomAD).

What do computational predictors say about BCAS4 p.Asp5Asn (c.13G>A)?

AlphaMissense predicts likely benign (score 0.1485) — an in-silico prediction, not a clinical call.

BCAS4 p.Asp5Asn

c.13G>A · rs1437457706 · VCV2266272

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1485 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000532%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1485	likely benign
REVEL	0.118	moderately benign-leaning
SaProt	LLR -6.96	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.3	GERP 0.48, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 82 kb · p 0.36 · regional, not allelic
Overall
CADD	20.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM D35N vs ClinVar D5N) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000532% European (non-Finnish) · 6/1,128,078 alleles

Filtering AF 0.000191% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000126%

Overall 0.000399% 6/1,504,774 alleles · very rare

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: BCAS4
Protein: p.Asp5Asn
Coding: c.13G>A
MANE Select: NM_198799
dbSNP: rs1437457706
Type: single nucleotide variant
Location: chr20:50795096 (GRCh38)
Gene constraint: LOEUF 1.081 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.40
Residue 5: the 'disordered' region

Full BCAS4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BCAS4 p.Ser130Thr Benign ★★ same type
BCAS4 p.Ser130Tyr Benign/Likely benign ★★ ⚠ same type
BCAS4 p.Thr142Met Likely benign ★★ same type
BCAS4 c.-15C>T Uncertain significance ★ ⚠ same type
BCAS4 c.-6C>T Uncertain significance ★ ⚠ same type
BCAS4 p.Ala118Ser Uncertain significance ★ ⚠ same type
BCAS4 p.Ala126Thr Uncertain significance ★ ⚠ same type
BCAS4 p.Ala29Ser 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/bcas4-p-asp5asn (accessed [today's date]).

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