Is CORO7-PAM16 p.Arg876Trp (c.2626C>T) pathogenic?

CORO7-PAM16 p.Arg876Trp (c.2626C>T) is classified Uncertain significance in CORO7-PAM16 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-16). AlphaMissense: likely benign (0.1196); Very rare (popmax 0.00458%, nfe).

How common is CORO7-PAM16 p.Arg876Trp (c.2626C>T) in the general population?

CORO7-PAM16 p.Arg876Trp (c.2626C>T) is very rare (popmax 0.00458%, nfe) (gnomAD).

What do computational predictors say about CORO7-PAM16 p.Arg876Trp (c.2626C>T)?

AlphaMissense predicts likely benign (score 0.1196) — an in-silico prediction, not a clinical call.

CORO7-PAM16 p.Arg876Trp

c.2626C>T · rs374424650 · VCV2457211

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1196 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00458%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1196	likely benign
REVEL	0.213	benign-leaning
SaProt	LLR -10.41	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3.2	GERP -0.54, phastCons 1
Overall
CADD	24.0	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 0.00458% European (non-Finnish) · 54/1,179,938 alleles

Filtering AF 0.00358% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00321%

Overall 0.00378% 61/1,613,720 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00458%	21,851
Admixed American	0.00333%	29,993
African / African-American	0.00267%	37,492
South Asian	0.0022%	45,523
Remaining individualsnot grpmax-eligible	0.0016%	62,500

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: CORO7-PAM16
Protein: p.Arg876Trp
Coding: c.2626C>T
MANE Select: NM_024535 · reported on NM_001201479
dbSNP: rs374424650
Type: single nucleotide variant
Location: chr16:4357227 (GRCh38)

Full CORO7-PAM16 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/coro7-pam16-p-arg876trp (accessed [today's date]).

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