chr4-113089932-G-T

Position:

• chr4-113089932-G-T

Variant summary

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

The NM_001148.6(ANK2):​c.84+40120G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,010 control chromosomes in the GnomAD database, including 17,566 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 0.47 (17566 hom., cov: 33)
• Consequence: ANK2 NM_001148.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANK2	NM_001148.6	c.84+40120G>T		intron_variant		ENST00000357077.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANK2	ENST00000357077.9	c.84+40120G>T		intron_variant		1	NM_001148.6	A2

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72074 AN: 151892 Hom.: 17555 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.474 AC: 72115 AN: 152010 Hom.: 17566 Cov.: 33 AF XY: 0.465 AC XY: 34566 AN XY: 74296

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.462

Alfa AF: 0.491 Hom.: 23914

Bravo AF: 0.461

Asia WGS AF: 0.323 AC: 1125 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.75

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

Other links and lift over

dbSNP: rs10029516; hg19: chr4-114011088;