rs1032913

Variant names:

• chr4-113017944-A-G
• rs1032913
• ENST00000506722.5:c.21+113430A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-113017944-A-G
• chr4-113017944-A-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+113430A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,196 control chromosomes in the GnomAD database, including 49,934 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 0.81 (49934 hom., cov: 33)
• Consequence: ANK2 ENST00000506722.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506722.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANK2	NM_001386142.1		c.21+113430A>G		intron	N/A	NP_001373071.1
	ANK2	NM_001386143.1		c.21+113430A>G		intron	N/A	NP_001373072.1
	ANK2	NM_001386186.2		c.73-156472A>G		intron	N/A	NP_001373115.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANK2	ENST00000506722.5	TSL:1	c.21+113430A>G		intron	N/A	ENSP00000421067.1
	ANK2	ENST00000672209.1		c.21+113430A>G		intron	N/A	ENSP00000499982.1
	ANK2	ENST00000673298.1		c.21+113430A>G		intron	N/A	ENSP00000500245.1

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123233 AN: 152078 Hom.: 49890 Cov.: 33

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.810 AC: 123338 AN: 152196 Hom.: 49934 Cov.: 33 AF XY: 0.812 AC XY: 60398 AN XY: 74404

African (AFR) AF: 0.825 AC: 34247 AN: 41536

American (AMR) AF: 0.860 AC: 13149 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2781 AN: 3468

East Asian (EAS) AF: 0.865 AC: 4476 AN: 5176

South Asian (SAS) AF: 0.866 AC: 4181 AN: 4828

European-Finnish (FIN) AF: 0.751 AC: 7944 AN: 10578

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53907 AN: 67996

Other (OTH) AF: 0.820 AC: 1734 AN: 2114

Alfa AF: 0.792 Hom.: 21254

Bravo AF: 0.820

Asia WGS AF: 0.878 AC: 3055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.79
DANN	Benign	0.47
PhyloP100		-1.0
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: rs1032913; hg19: chr4-113939100;