Is BIVM p.Ile82Val (c.244A>G) pathogenic?

BIVM p.Ile82Val (c.244A>G) is classified Benign in BIVM (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-01). AlphaMissense: likely benign (0.0626); Low-frequency (popmax 1.01%, nfe).

How common is BIVM p.Ile82Val (c.244A>G) in the general population?

BIVM p.Ile82Val (c.244A>G) is low-frequency (popmax 1.01%, nfe) (gnomAD).

What do computational predictors say about BIVM p.Ile82Val (c.244A>G)?

AlphaMissense predicts likely benign (score 0.0626) — an in-silico prediction, not a clinical call.

BIVM p.Ile82Val

c.244A>G · rs41281670 · VCV1686561

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0626 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.01%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0626	likely benign
REVEL	0.018	moderately benign-leaning
SaProt	LLR -6.18	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 0.81	GERP -3.7, phastCons 0.5
Regional constraint	o/e 0.91	unconstrained · MANE · 15 kb · p 0.087 · regional, not allelic
Overall
CADD	3.38	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 1.01% European (non-Finnish) · 11,894/1,180,034 alleles

Filtering AF 0.993% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.986%

Overall 0.808% 13,048/1,614,190 alleles · low-frequency

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	1.01%	99
Remaining individualsnot grpmax-eligible	0.605%	165
Amishnot grpmax-eligible	0.548%	182
Ashkenazi Jewishnot grpmax-eligible	0.345%	290
Finnishnot grpmax-eligible	0.264%	379
Admixed American	0.247%	406
South Asian	0.239%	418
Middle Eastern	0.231%	433
African / African-American	0.159%	631
East Asian	0.00223%	44,886

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: BIVM
Protein: p.Ile82Val
Coding: c.244A>G
MANE Select: NM_017693
dbSNP: rs41281670
Type: single nucleotide variant
Location: chr13:102807511 (GRCh38)
Gene constraint: LOEUF 0.669 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.50

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

Similar variants

BIVM p.Gly463= Benign ★★ same type
BIVM p.Ser477Leu Likely benign ★★ same type
BIVM-ERCC5 p.Ser117Leu Uncertain significance ★ ⚠ same type
BIVM p.Ala79Val Uncertain significance ★ ⚠ same type
BIVM p.Asn11Asp Uncertain significance ★ ⚠ same type
BIVM p.Asn234Lys Uncertain significance ★ ⚠ same type
BIVM p.Gly14Arg Uncertain significance ★ ⚠ same type
BIVM p.Gly492Ala 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/bivm-p-ile82val (accessed [today's date]).

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