Is AFF2 p.Ser387Tyr (c.1160C>A) pathogenic?

AFF2 p.Ser387Tyr (c.1160C>A) is classified Likely benign in AFF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-01). AlphaMissense: likely benign (0.1194); Ultra-rare (popmax 0.0238%, eas).

How common is AFF2 p.Ser387Tyr (c.1160C>A) in the general population?

AFF2 p.Ser387Tyr (c.1160C>A) is ultra-rare (popmax 0.0238%, eas) (gnomAD).

What do computational predictors say about AFF2 p.Ser387Tyr (c.1160C>A)?

AlphaMissense predicts likely benign (score 0.1194) — an in-silico prediction, not a clinical call.

AFF2 p.Ser387Tyr

c.1160C>A · rs373013286 · VCV2661603

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1194 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0238%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1194	likely benign
REVEL	0.14	moderately benign-leaning
SaProt	LLR -8.47	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 0.008, phastCons 0.02
Regional constraint	o/e 0.94	unconstrained · MANE · 304 kb · p 0.17 · regional, not allelic
Overall
CADD	20.5	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 0.0238% East Asian · 8/33,615 alleles

Filtering AF 0.0118% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00864%

Overall 0.00152% 18/1,186,560 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0238%	4,202
Remaining individualsnot grpmax-eligible	0.0064%	15,626
European (non-Finnish)	0.0008%	124,933

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: AFF2
Protein: p.Ser387Tyr
Coding: c.1160C>A
MANE Select: NM_002025
dbSNP: rs373013286
Type: single nucleotide variant
Location: chrX:148837720 (GRCh38)
Structure: AlphaFold pLDDT 49.27
Residue 387: the 'disordered' region

Full AFF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AFF2 c.3267+5G>C Uncertain significance ★★ same type
AFF2 p.Ala1197Thr Uncertain significance ★★ ⚠ same type
AFF2 p.Ala171Pro Uncertain significance ★★ ⚠ same type
AFF2 p.Arg1238Cys Uncertain significance ★★ ⚠ same type
AFF2 p.Arg1295Cys Uncertain significance ★★ ⚠ same type
AFF2 p.Arg670His Uncertain significance ★★ ⚠ same type
AFF2 p.Asn77Ile Uncertain significance ★★ ⚠ same type
AFF2 p.Asp187Glu 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/aff2-p-ser387tyr (accessed [today's date]).

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