Is ANK2 p.Ile3930= (c.11790C>T) pathogenic?

ANK2 p.Ile3930= (c.11790C>T) is classified Benign in ANK2 (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-02-04). Low-frequency (popmax 2.94%, afr); Associated with Cardiovascular phenotype.

What condition is associated with ANK2 p.Ile3930= (c.11790C>T)?

ANK2 p.Ile3930= (c.11790C>T) is associated with Cardiovascular phenotype, long QT syndrome, cardiac arrhythmia, ankyrin-B-related (ClinVar).

How common is ANK2 p.Ile3930= (c.11790C>T) in the general population?

ANK2 p.Ile3930= (c.11790C>T) is low-frequency (popmax 2.94%, afr) (gnomAD).

ANK2 p.Ile3930=

c.11790C>T · rs45517840 · VCV136398

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.94%, afr)

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 -3.4	GERP -5.7
Overall
CADD	5.707	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.94% African / African-American · 2,203/75,016 alleles

Filtering AF 2.83% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.79%

Overall 0.252% 4,073/1,614,106 alleles · low-frequency

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	3.35%	30
African / African-Americangrpmax	2.94%	34
Middle Eastern	0.544%	184
Remaining individualsnot grpmax-eligible	0.475%	210
Admixed American	0.263%	380
South Asian	0.034%	2,938
European (non-Finnish)	0.0295%	3,391
East Asian	0.0178%	5,610
Finnishnot grpmax-eligible	0.00312%	32,010

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ANK2
Protein: p.Ile3930=
Coding: c.11790C>T
MANE Select: NM_001148
dbSNP: rs45517840
Type: single nucleotide variant
Location: chr4:113373380 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

Full ANK2 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: long QT syndrome cardiac arrhythmia, ankyrin-B-related

Similar variants

ANK2 p.Ile3930Met Uncertain significance ★ ⚠ same residue
ANK2 p.Arg1007Ter Pathogenic/Likely pathogenic ★★ same condition
ANK2 p.Arg1088Ter Pathogenic ★★ same condition
ANK2 p.Arg3113Ter Pathogenic ★★ same condition
ANK2 p.Arg895Ter Pathogenic/Likely pathogenic ★★ same condition
ANK2 p.Arg977Ter Pathogenic ★★ same condition
ANK2 c.11032+11G>T Uncertain significance ★★ same condition
ANK2 c.11611-3T>A 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/ank2-p-ile3930 (accessed [today's date]).

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