4-113049622-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000506722.5(ANK2):​c.22-124794A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000446 in 1,216,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.000014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00045 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ANK2
ENST00000506722.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.659
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-AS1 (HGNC:40076): (ANK2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 4-113049622-A-C is Benign according to our data. Variant chr4-113049622-A-C is described in ClinVar as [Benign]. Clinvar id is 1292223.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 542 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ANK2NM_001148.6 linkuse as main transcript upstream_gene_variant ENST00000357077.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ANK2-AS1ENST00000508959.1 linkuse as main transcriptn.126-14828T>G intron_variant, non_coding_transcript_variant 2
ANK2ENST00000357077.9 linkuse as main transcript upstream_gene_variant 1 NM_001148.6 A2Q01484-4

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
2
AN:
146890
Hom.:
0
Cov.:
32
FAILED QC
Gnomad AFR
AF:
0.0000506
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000446
AC:
542
AN:
1216030
Hom.:
0
Cov.:
31
AF XY:
0.000468
AC XY:
281
AN XY:
599844
show subpopulations
Gnomad4 AFR exome
AF:
0.000702
Gnomad4 AMR exome
AF:
0.000344
Gnomad4 ASJ exome
AF:
0.00131
Gnomad4 EAS exome
AF:
0.00202
Gnomad4 SAS exome
AF:
0.0000388
Gnomad4 FIN exome
AF:
0.00104
Gnomad4 NFE exome
AF:
0.000383
Gnomad4 OTH exome
AF:
0.000696
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000136
AC:
2
AN:
147010
Hom.:
0
Cov.:
32
AF XY:
0.0000140
AC XY:
1
AN XY:
71430
show subpopulations
Gnomad4 AFR
AF:
0.0000505
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMar 03, 2015- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
CADD
Benign
17
DANN
Benign
0.64

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-113970778; API