NM_001148.6:c.9900C>A

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001148.6(ANK2):c.9900C>A(p.Ser3300Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0249 in 1,614,042 control chromosomes in the GnomAD database, including 586 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 34 hom., cov: 32)

Exomes 𝑓: 0.025 ( 552 hom. )

Consequence

ANK2
NM_001148.6 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:12

Conservation

PhyloP100: 2.14

Variant links:

Genes affected

ANK2 (HGNC:493): (ankyrin 2) This gene encodes a member of the ankyrin family of proteins that link the integral membrane proteins to the underlying spectrin-actin cytoskeleton. Ankyrins play key roles in activities such as cell motility, activation, proliferation, contact and the maintenance of specialized membrane domains. Most ankyrins are typically composed of three structural domains: an amino-terminal domain containing multiple ankyrin repeats; a central region with a highly conserved spectrin binding domain; and a carboxy-terminal regulatory domain which is the least conserved and subject to variation. The protein encoded by this gene is required for targeting and stability of Na/Ca exchanger 1 in cardiomyocytes. Mutations in this gene cause long QT syndrome 4 and cardiac arrhythmia syndrome. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Dec 2011]

ANK2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006141901).

BP6

Variant 4-113358518-C-A is Benign according to our data. Variant chr4-113358518-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 191563.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-113358518-C-A is described in Lovd as [Benign]. Variant chr4-113358518-C-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0194 (2961/152270) while in subpopulation NFE AF= 0.0296 (2013/68012). AF 95% confidence interval is 0.0285. There are 34 homozygotes in gnomad4. There are 1435 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 2961 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANK2	NM_001148.6 link	c.9900C>A	p.Ser3300Arg	missense_variant	Exon 38 of 46	ENST00000357077.9	NP_001139.3	Q01484-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANK2	ENST00000357077.9 link	c.9900C>A	p.Ser3300Arg	missense_variant	Exon 38 of 46	1	NM_001148.6	ENSP00000349588.4		Q01484-4

Frequencies

GnomAD3 genomes

AF:

0.0195

AC:

2964

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00528

Gnomad AMI

AF:

0.0275

Gnomad AMR

AF:

0.0139

Gnomad ASJ

AF:

0.0193

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.00974

Gnomad FIN

AF:

0.0318

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0296

Gnomad OTH

AF:

0.0182

GnomAD3 exomes

AF:

0.0192

AC:

4793

AN:

250094

Hom.:

AF XY:

0.0195

AC XY:

2642

AN XY:

135204

show subpopulations

Gnomad AFR exome

AF:

0.00450

Gnomad AMR exome

AF:

0.0123

Gnomad ASJ exome

AF:

0.0187

Gnomad EAS exome

AF:

0.000436

Gnomad SAS exome

AF:

0.00869

Gnomad FIN exome

AF:

0.0297

Gnomad NFE exome

AF:

0.0271

Gnomad OTH exome

AF:

0.0219

GnomAD4 exome

AF:

0.0255

AC:

37256

AN:

1461772

Hom.:

552

Cov.:

AF XY:

0.0250

AC XY:

18173

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.00448

Gnomad4 AMR exome

AF:

0.0125

Gnomad4 ASJ exome

AF:

0.0176

Gnomad4 EAS exome

AF:

0.000252

Gnomad4 SAS exome

AF:

0.00869

Gnomad4 FIN exome

AF:

0.0330

Gnomad4 NFE exome

AF:

0.0288

Gnomad4 OTH exome

AF:

0.0243

GnomAD4 genome

AF:

0.0194

AC:

2961

AN:

152270

Hom.:

Cov.:

AF XY:

0.0193

AC XY:

1435

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00527

Gnomad4 AMR

AF:

0.0139

Gnomad4 ASJ

AF:

0.0193

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.00954

Gnomad4 FIN

AF:

0.0318

Gnomad4 NFE

AF:

0.0296

Gnomad4 OTH

AF:

0.0180

Alfa

AF:

0.0252

Hom.:

Bravo

AF:

0.0171

TwinsUK

AF:

0.0283

AC:

105

ALSPAC

AF:

0.0384

AC:

148

ESP6500AA

AF:

0.00522

AC:

ESP6500EA

AF:

0.0317

AC:

273

ExAC

AF:

0.0188

AC:

2278

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.0275

EpiControl

AF:

0.0271

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ANK2: BS1, BS2 -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 29, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:3

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 24, 2013

Biesecker Lab/Clinical Genomics Section, National Institutes of Health

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: research

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiac arrhythmia, ankyrin-B-related

Benign:3

Dec 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Oct 09, 2014

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Long QT syndrome

Benign:1

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype

Benign:1

Jul 27, 2015

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.42

BayesDel_addAF

Benign

-0.21

BayesDel_noAF

Uncertain

-0.050

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.34

T;T;T

Eigen

Benign

0.020

Eigen_PC

Benign

0.017

FATHMM_MKL

Uncertain

0.83

LIST_S2

Uncertain

0.88

D;D;D

MetaRNN

Benign

0.0061

T;T;T

MetaSVM

Uncertain

0.40

MutationAssessor

Uncertain

2.4

M;.;.

PrimateAI

Benign

0.34

PROVEAN

Benign

-1.6

N;N;N

REVEL

Benign

0.27

Sift

Uncertain

0.0050

D;D;D

Sift4G

Benign

0.40

T;T;D

Vest4

0.22

MutPred

0.27

.;Gain of glycosylation at Y3266 (P = 0.0017);.;

MPC

0.19

ClinPred

0.016

GERP RS

4.1

Varity_R

0.20

gMVP

0.082

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over