Is ANKRD20A1 p.Asp545= (c.1635C>T) pathogenic?

ANKRD20A1 p.Asp545= (c.1635C>T) is classified Likely benign in ANKRD20A1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-01). Rare (popmax 0.218%, mid).

How common is ANKRD20A1 p.Asp545= (c.1635C>T) in the general population?

ANKRD20A1 p.Asp545= (c.1635C>T) is rare (popmax 0.218%, mid) (gnomAD).

ANKRD20A1 p.Asp545=

c.1635C>T · rs551564604 · VCV2659228

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.218%, mid)

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 -10	GERP -0.54
Overall
CADD	0.244	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.218% Middle Eastern · 7/3,210 alleles

Filtering AF 0.102% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0726%

Overall 0.02% 207/1,032,650 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.218%	459
Admixed American	0.0912%	1,096
South Asian	0.0837%	1,195
Remaining individualsnot grpmax-eligible	0.0388%	2,577
European (non-Finnish)	0.0137%	7,306
African / African-American	0.00533%	18,779

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: ANKRD20A1
Protein: p.Asp545=
Coding: c.1635C>T
MANE Select: NM_032250
dbSNP: rs551564604
Type: single nucleotide variant
Location: chr9:67900630 (GRCh38)
Gene constraint: LOEUF 0.512 · pLI 0.94 (gnomAD)
Structure: AlphaFold pLDDT 69.38

Full ANKRD20A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ANKRD20A1 p.Ala173= Likely benign ★ same type
ANKRD20A1 p.Asp756= Likely benign ★ same type
ANKRD20A1 p.His620Tyr Likely benign ★ 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/ankrd20a1-p-asp545 (accessed [today's date]).

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