Is BCCIP p.Asp68Val (c.203A>T) pathogenic?

BCCIP p.Asp68Val (c.203A>T) is classified Uncertain significance in BCCIP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-16). AlphaMissense: likely benign (0.1214); Ultra-rare (popmax 0.0103%, nfe).

How common is BCCIP p.Asp68Val (c.203A>T) in the general population?

BCCIP p.Asp68Val (c.203A>T) is ultra-rare (popmax 0.0103%, nfe) (gnomAD).

What do computational predictors say about BCCIP p.Asp68Val (c.203A>T)?

AlphaMissense predicts likely benign (score 0.1214) — an in-silico prediction, not a clinical call.

BCCIP p.Asp68Val

c.203A>T · VCV4828196

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1214 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0103%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1214	likely benign
REVEL	0.214	benign-leaning
SaProt	LLR -12.06	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>G here scores Δ0.76 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.5	GERP -1
Regional constraint	o/e 1.00	unconstrained · MANE · 13 kb · p 0.93 · regional, not allelic
Overall
CADD	22.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0103% European (non-Finnish) · 122/1,179,842 alleles

Filtering AF 0.00884% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00828%

Overall 0.00818% 132/1,613,648 alleles · ultra-rare exomes 127/1,461,462 · genomes 5/152,186 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0128%	7,808
European (non-Finnish)grpmax	0.0103%	9,671
Admixed American	0.00333%	29,993

Remaining individuals 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: BCCIP
Protein: p.Asp68Val
Coding: c.203A>T
MANE Select: NM_078468
Type: single nucleotide variant
Location: chr10:125826628 (GRCh38)
Gene constraint: LOEUF 1.053 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.67 · 5 PDB
Residue 68: an α-helix; the 'interaction with brca2' region

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

Similar variants

DHX32 p.Ala496Val Uncertain significance ★★ ⚠ same type
DHX32 p.Ala510Thr Uncertain significance ★★ ⚠ same type
DHX32 p.Ala529Ser Uncertain significance ★★ ⚠ same type
DHX32 p.Ala619Thr Uncertain significance ★★ ⚠ same type
DHX32 p.Arg572Cys Uncertain significance ★★ ⚠ same type
DHX32 p.Asn448Lys Uncertain significance ★★ ⚠ same type
DHX32 p.Asn473His Uncertain significance ★★ ⚠ same type
DHX32 p.Asp585Ala 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/bccip-p-asp68val (accessed [today's date]).

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