Is ASNS c.487+2TAA[2] pathogenic?

ASNS c.487+2TAA[2] is classified Likely benign in ASNS (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-09). Very rare (popmax 0.00527%, amr).

How common is ASNS c.487+2TAA[2] in the general population?

ASNS c.487+2TAA[2] is very rare (popmax 0.00527%, amr) (gnomAD).

ASNS c.487+2TAA[2]

rs1562820219 · VCV1647879

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

canonical splice-site (±1/±2)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00527%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	canonical splice-site (±1/±2)	predicted loss-of-function
Splicing
Splice region	donor +2	canonical splice dinucleotide (donor +2) · inside the BP7-excluded zone
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2.8	GERP -2.1
Non-coding constraint	Z 2.05	1 kb window · o/e 0.85 · regional · uncalibrated
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00527% Admixed American · 3/56,894 alleles

Filtering AF 0.0014% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000688%

Overall 0.000278% 4/1,440,184 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00527%	18,965
Remaining individualsnot grpmax-eligible	0.00163%	61,498

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: ASNS
Coding: c.487+2TAA[2]
MANE Select: NM_001673
dbSNP: rs1562820219
Type: Microsatellite
Location: chr7:97864249 (GRCh38)
Gene constraint: LOEUF 0.745 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.36 · 3 PDB

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

Similar variants

ASNS p.Asp250fs Pathogenic/Likely pathogenic ★★ same type
ASNS p.Leu393fs Likely pathogenic ★ same type
ASNS p.Phe134fs Pathogenic ★ same type
ASNS p.Val231fs Pathogenic ★ same type
ASNS c.1239-15_1239-13del Likely benign ★ same type
ASNS c.903+15_903+16del Likely benign ★ same type
ASNS p.Glu389del 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/asns-c-487-plus-2taa-2 (accessed [today's date]).

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