rs10155204

Variant names:

• chr4-113036858-C-T
• rs10155204
• ENST00000506722.5:c.21+132344C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506722.5(ANK2):​c.21+132344C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 151,654 control chromosomes in the GnomAD database, including 51,926 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.82 (51926 hom., cov: 30)
• Consequence: ANK2 ENST00000506722.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 2 publications found

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)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANK2	NM_001386142.1	c.21+132344C>T		intron_variant	Intron 2 of 44		NP_001373071.1
ANK2	NM_001386143.1	c.21+132344C>T		intron_variant	Intron 2 of 47		NP_001373072.1
ANK2	NM_001386186.2	c.73-137558C>T		intron_variant	Intron 1 of 46		NP_001373115.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANK2	ENST00000506722.5	c.21+132344C>T		intron_variant	Intron 2 of 46	1		ENSP00000421067.1
ANK2	ENST00000672209.1	c.21+132344C>T		intron_variant	Intron 2 of 47			ENSP00000499982.1
ANK2	ENST00000673298.1	c.21+132344C>T		intron_variant	Intron 2 of 46			ENSP00000500245.1

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124582 AN: 151536 Hom.: 51901 Cov.: 30

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.836

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.822 AC: 124653 AN: 151654 Hom.: 51926 Cov.: 30 AF XY: 0.826 AC XY: 61203 AN XY: 74080

African (AFR) AF: 0.671 AC: 27756 AN: 41340

American (AMR) AF: 0.903 AC: 13727 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2937 AN: 3466

East Asian (EAS) AF: 0.970 AC: 4928 AN: 5082

South Asian (SAS) AF: 0.862 AC: 4149 AN: 4816

European-Finnish (FIN) AF: 0.883 AC: 9316 AN: 10552

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59035 AN: 67882

Other (OTH) AF: 0.838 AC: 1765 AN: 2106

Alfa AF: 0.834 Hom.: 8700

Bravo AF: 0.819

Asia WGS AF: 0.901 AC: 3133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.29
DANN	Benign	0.40
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10155204; hg19: chr4-113958014;