Is ANKRD7 p.Ala68Thr (c.202G>A) pathogenic?

ANKRD7 p.Ala68Thr (c.202G>A) is classified Uncertain significance in ANKRD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-25). AlphaMissense: likely benign (0.19); Ultra-rare (popmax 0.0327%, nfe).

How common is ANKRD7 p.Ala68Thr (c.202G>A) in the general population?

ANKRD7 p.Ala68Thr (c.202G>A) is ultra-rare (popmax 0.0327%, nfe) (gnomAD).

What do computational predictors say about ANKRD7 p.Ala68Thr (c.202G>A)?

AlphaMissense predicts likely benign (score 0.19) — an in-silico prediction, not a clinical call.

ANKRD7 p.Ala68Thr

c.202G>A · rs370288583 · VCV2387276

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.19 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0327%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.19	likely benign
REVEL	0.321	indeterminate
SaProt	LLR -10.04	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.2	GERP 1.3, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 15 kb · p 0.065 · regional, not allelic
Overall
CADD	23.4	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 0.0327% European (non-Finnish) · 385/1,178,978 alleles

Filtering AF 0.03% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0289%

Overall 0.0248% 399/1,611,246 alleles · ultra-rare exomes 385/1,459,068 · genomes 14/152,178 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0327%	3,062
Remaining individualsnot grpmax-eligible	0.0144%	6,930
African / African-American	0.00535%	18,702
Finnishnot grpmax-eligible	0.00156%	63,988

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: ANKRD7
Protein: p.Ala68Thr
Coding: c.202G>A
MANE Select: NM_019644
dbSNP: rs370288583
Type: single nucleotide variant
Location: chr7:118234453 (GRCh38)
Gene constraint: LOEUF 1.219 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.97

Full ANKRD7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANKRD7 p.Ala99Ser Uncertain significance ★ ⚠ same type
ANKRD7 p.Arg124Cys Uncertain significance ★ ⚠ same type
ANKRD7 p.Arg124His Uncertain significance ★ ⚠ same type
ANKRD7 p.Arg22Gln Uncertain significance ★ ⚠ same type
ANKRD7 p.Arg22Pro Uncertain significance ★ ⚠ same type
ANKRD7 p.Asn20Lys Uncertain significance ★ ⚠ same type
ANKRD7 p.Asp117Asn Uncertain significance ★ ⚠ same type
ANKRD7 p.Gln17Lys 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/ankrd7-p-ala68thr (accessed [today's date]).

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