Is ABCF1 p.Arg396Gln (c.1187G>A) pathogenic?

ABCF1 p.Arg396Gln (c.1187G>A) is classified Benign in ABCF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-26). AlphaMissense: likely benign (0.0639); Low-frequency (popmax 1.64%, afr).

How common is ABCF1 p.Arg396Gln (c.1187G>A) in the general population?

ABCF1 p.Arg396Gln (c.1187G>A) is low-frequency (popmax 1.64%, afr) (gnomAD).

What do computational predictors say about ABCF1 p.Arg396Gln (c.1187G>A)?

AlphaMissense predicts likely benign (score 0.0639) — an in-silico prediction, not a clinical call.

ABCF1 p.Arg396Gln

c.1187G>A · rs61741255 · VCV714311

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0639 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.64%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0639	likely benign
REVEL	0.166	moderately benign-leaning
SaProt	LLR -6.12	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 -0.13
Regional constraint	o/e 0.64	unconstrained · MANE · 2,182 bp · p 7.6e-09 · regional, not allelic
Overall
CADD	10.9	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 1.64% African / African-American · 1,229/74,992 alleles

Filtering AF 1.56% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.53%

Overall 0.0916% 1,477/1,613,058 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.64%	61
Admixed American	0.127%	790
Remaining individualsnot grpmax-eligible	0.102%	977
Middle Eastern	0.0495%	2,021
Ashkenazi Jewishnot grpmax-eligible	0.0304%	3,290
South Asian	0.00769%	13,010
European (non-Finnish)	0.00746%	13,409
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: ABCF1
Protein: p.Arg396Gln
Coding: c.1187G>A
MANE Select: NM_001025091
dbSNP: rs61741255
Type: single nucleotide variant
Location: chr6:30584276 (GRCh38)
Gene constraint: LOEUF 0.69 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.68 · 1 PDB
Residue 396: the abc transporter 1 domain; an α-helix

Full ABCF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCF1 p.Ala117Thr Uncertain significance ★ ⚠ same type
ABCF1 p.Ala194Thr Uncertain significance ★ ⚠ same type
ABCF1 p.Ala221Thr Uncertain significance ★ ⚠ same type
ABCF1 p.Ala251Thr Uncertain significance ★ ⚠ same type
ABCF1 p.Ala276Val Uncertain significance ★ ⚠ same type
ABCF1 p.Ala328Asp Uncertain significance ★ ⚠ same type
ABCF1 p.Ala427Thr Uncertain significance ★ ⚠ same type
ABCF1 p.Ala598Gly 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/abcf1-p-arg396gln (accessed [today's date]).

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