rs35728190

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001148.6(ANK2):c.10888+20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,612,242 control chromosomes in the GnomAD database, including 9,285 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 923 hom., cov: 32)

Exomes 𝑓: 0.10 ( 8362 hom. )

Consequence

ANK2
NM_001148.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: -0.838

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 (BayesDel_noAF=-0.91).

BP6

Variant 4-113363489-C-T is Benign according to our data. Variant chr4-113363489-C-T is described in ClinVar as [Benign]. Clinvar id is 136394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-113363489-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANK2	NM_001148.6 link	c.10888+20C>T		intron_variant	Intron 40 of 45	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.10888+20C>T		intron_variant	Intron 40 of 45	1	NM_001148.6	ENSP00000349588.4		Q01484-4

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

16000

AN:

152056

Hom.:

923

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.0516

Gnomad AMR

AF:

0.0874

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0267

Gnomad FIN

AF:

0.0996

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.123

GnomAD3 exomes

AF:

0.0896

AC:

22487

AN:

251068

Hom.:

1241

AF XY:

0.0901

AC XY:

12223

AN XY:

135692

show subpopulations

Gnomad AFR exome

AF:

0.116

Gnomad AMR exome

AF:

0.0613

Gnomad ASJ exome

AF:

0.123

Gnomad EAS exome

AF:

0.000435

Gnomad SAS exome

AF:

0.0352

Gnomad FIN exome

AF:

0.104

Gnomad NFE exome

AF:

0.117

Gnomad OTH exome

AF:

0.113

GnomAD4 exome

AF:

0.103

AC:

150601

AN:

1460068

Hom.:

8362

Cov.:

AF XY:

0.102

AC XY:

74297

AN XY:

726374

show subpopulations

Gnomad4 AFR exome

AF:

0.119

Gnomad4 AMR exome

AF:

0.0641

Gnomad4 ASJ exome

AF:

0.119

Gnomad4 EAS exome

AF:

0.000303

Gnomad4 SAS exome

AF:

0.0356

Gnomad4 FIN exome

AF:

0.106

Gnomad4 NFE exome

AF:

0.112

Gnomad4 OTH exome

AF:

0.104

GnomAD4 genome

AF:

0.105

AC:

16008

AN:

152174

Hom.:

923

Cov.:

AF XY:

0.103

AC XY:

7637

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.0872

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0269

Gnomad4 FIN

AF:

0.0996

Gnomad4 NFE

AF:

0.118

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.119

Hom.:

194

Bravo

AF:

0.106

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Mar 04, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiac arrhythmia, ankyrin-B-related

Benign:2

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Dec 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Long QT syndrome

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.099

DANN

Benign

0.20

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