Is ANKRD1 p.Ala50= (c.150C>G) pathogenic?

ANKRD1 p.Ala50= (c.150C>G) is classified Benign/Likely benign in ANKRD1 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-01-08). Low-frequency (popmax 1.05%, sas); Associated with Cardiovascular phenotype.

What condition is associated with ANKRD1 p.Ala50= (c.150C>G)?

ANKRD1 p.Ala50= (c.150C>G) is associated with Cardiovascular phenotype, congenital total pulmonary venous return anomaly (ClinVar).

How common is ANKRD1 p.Ala50= (c.150C>G) in the general population?

ANKRD1 p.Ala50= (c.150C>G) is low-frequency (popmax 1.05%, sas) (gnomAD).

ANKRD1 p.Ala50=

c.150C>G · rs147484763 · VCV178005

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.05%, sas)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.74	GERP -3, phastCons 0.13
Overall
CADD	7.363	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.05% South Asian · 955/91,016 alleles

Filtering AF 0.994% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.972%

Overall 0.0646% 1,043/1,613,974 alleles · low-frequency

Ancestry group	Frequency	1 in
South Asiangrpmax	1.05%	95
Remaining individualsnot grpmax-eligible	0.102%	977
Middle Eastern	0.0331%	3,019
African / African-American	0.004%	25,001
Finnishnot grpmax-eligible	0.00312%	32,017
European (non-Finnish)	0.00144%	69,412

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: ANKRD1
Protein: p.Ala50=
Coding: c.150C>G
MANE Select: NM_014391
dbSNP: rs147484763
Type: single nucleotide variant
Location: chr10:90920226 (GRCh38)
Gene constraint: LOEUF 1.038 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.64

Full ANKRD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: congenital total pulmonary venous return anomaly

Similar variants

ANKRD1 p.Ala50Pro Benign/Likely benign ★★ same residue
ANKRD1 p.Ala50Ser Uncertain significance ★ ⚠ same residue
ANKRD1 p.Ala50Asp Uncertain significance ★ ⚠ same residue
ANKRD1 c.207+1G>T Uncertain significance ★★ same condition
ANKRD1 c.27+1G>T Uncertain significance ★★ same condition
ANKRD1 c.28-3T>C Uncertain significance ★★ same condition
ANKRD1 c.651+4T>A Uncertain significance ★★ same condition
ANKRD1 c.750+2T>C Uncertain significance ★★ same condition

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/ankrd1-p-ala50 (accessed [today's date]).

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