Is ABHD16B p.Val7Met (c.19G>A) pathogenic?

ABHD16B p.Val7Met (c.19G>A) is classified Uncertain significance in ABHD16B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-14). AlphaMissense: likely benign (0.0956); Rare (popmax 0.117%, mid).

How common is ABHD16B p.Val7Met (c.19G>A) in the general population?

ABHD16B p.Val7Met (c.19G>A) is rare (popmax 0.117%, mid) (gnomAD).

What do computational predictors say about ABHD16B p.Val7Met (c.19G>A)?

AlphaMissense predicts likely benign (score 0.0956) — an in-silico prediction, not a clinical call.

ABHD16B p.Val7Met

c.19G>A · rs141688971 · VCV2342635

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0956 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.117%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0956	likely benign
REVEL	0.048	moderately benign-leaning
SaProt	LLR -8.45	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 1.4	GERP -3.7, phastCons 0.87
Regional constraint	o/e 1.06	unconstrained · MANE · 1,406 bp · p 0.089 · regional, not allelic
Overall
CADD	18.22	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.117% Middle Eastern · 7/5,984 alleles

Filtering AF 0.0577% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.052%

Overall 0.0216% 336/1,556,402 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.117%	855
African / African-American	0.0733%	1,363
Admixed American	0.0663%	1,509
Remaining individualsnot grpmax-eligible	0.0281%	3,557
European (non-Finnish)	0.0193%	5,171

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: ABHD16B
Protein: p.Val7Met
Coding: c.19G>A
MANE Select: NM_080622
dbSNP: rs141688971
Type: single nucleotide variant
Location: chr20:63861559 (GRCh38)
Gene constraint: LOEUF 1.955 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.64

Full ABHD16B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABHD16B p.Val7Gly Uncertain significance ★ ⚠ same residue
ABHD16B p.Ala143Pro Uncertain significance ★ ⚠ same type
ABHD16B p.Ala147Gly Uncertain significance ★ ⚠ same type
ABHD16B p.Ala181Thr Uncertain significance ★ ⚠ same type
ABHD16B p.Ala195Thr Uncertain significance ★ ⚠ same type
ABHD16B p.Ala20Ser Uncertain significance ★ ⚠ same type
ABHD16B p.Ala239Val Uncertain significance ★ ⚠ same type
ABHD16B p.Ala253Gly 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/abhd16b-p-val7met (accessed [today's date]).

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