4-112947451-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506722.5(ANK2):c.21+42937T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,926 control chromosomes in the GnomAD database, including 13,984 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 0.40 (13984 hom., cov: 32)
• Consequence: ANK2 ENST00000506722.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANK2	NM_001127493.3	c.21+42937T>G		intron_variant
ANK2	NM_001354239.2	c.21+42937T>G		intron_variant
ANK2	NM_001354243.2	c.21+42937T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANK2	ENST00000506722.5	c.21+42937T>G		intron_variant		1
ANK2	ENST00000503271.5	c.21+42937T>G		intron_variant		2
ANK2	ENST00000503423.6	c.21+42937T>G		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60529 AN: 151808 Hom.: 13966 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.399 AC: 60590 AN: 151926 Hom.: 13984 Cov.: 32 AF XY: 0.402 AC XY: 29840 AN XY: 74272

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.356

Alfa AF: 0.293 Hom.: 6999

Bravo AF: 0.418

Asia WGS AF: 0.419 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.27
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7678728; hg19: chr4-113868607;