Variant rs58762441 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_014391.3(ANKRD1):c.346-19_346-14del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 301,188 control chromosomes in the GnomAD database, including 4,516 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 2543 hom., cov: 0)

Exomes 𝑓: 0.14 ( 1973 hom. )

Consequence

ANKRD1
NM_014391.3 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 3.19

Variant links:

Genes affected

ANKRD1 (HGNC:15819): (ankyrin repeat domain 1) The protein encoded by this gene is localized to the nucleus of endothelial cells and is induced by IL-1 and TNF-alpha stimulation. Studies in rat cardiomyocytes suggest that this gene functions as a transcription factor. Interactions between this protein and the sarcomeric proteins myopalladin and titin suggest that it may also be involved in the myofibrillar stretch-sensor system. [provided by RefSeq, Jul 2008]

ANKRD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 10-90918985-TAAATAA-T is Benign according to our data. Variant chr10-90918985-TAAATAA-T is described in ClinVar as [Benign]. Clinvar id is 45632.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-90918985-TAAATAA-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD1	NM_014391.3 linkuse as main transcript	c.346-19_346-14del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000371697.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD1	ENST00000371697.4 linkuse as main transcript	c.346-19_346-14del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_014391.3	P1

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

17302

AN:

63404

Hom.:

2543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.406

Gnomad AMI

AF:

0.0385

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.392

Gnomad SAS

AF:

0.320

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.268

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.251

GnomAD3 exomes

AF:

0.0514

AC:

10913

AN:

212278

Hom.:

2160

AF XY:

0.0495

AC XY:

5726

AN XY:

115692

show subpopulations

Gnomad AFR exome

AF:

0.183

Gnomad AMR exome

AF:

0.0434

Gnomad ASJ exome

AF:

0.0311

Gnomad EAS exome

AF:

0.112

Gnomad SAS exome

AF:

0.0664

Gnomad FIN exome

AF:

0.0458

Gnomad NFE exome

AF:

0.0297

Gnomad OTH exome

AF:

0.0367

GnomAD4 exome

AF:

0.143

AC:

34049

AN:

237782

Hom.:

1973

AF XY:

0.144

AC XY:

17244

AN XY:

119524

show subpopulations

Gnomad4 AFR exome

AF:

0.403

Gnomad4 AMR exome

AF:

0.350

Gnomad4 ASJ exome

AF:

0.143

Gnomad4 EAS exome

AF:

0.339

Gnomad4 SAS exome

AF:

0.281

Gnomad4 FIN exome

AF:

0.177

Gnomad4 NFE exome

AF:

0.0993

Gnomad4 OTH exome

AF:

0.172

GnomAD4 genome

AF:

0.273

AC:

17302

AN:

63406

Hom.:

2543

Cov.:

AF XY:

0.280

AC XY:

8573

AN XY:

30570

show subpopulations

Gnomad4 AFR

AF:

0.405

Gnomad4 AMR

AF:

0.301

Gnomad4 ASJ

AF:

0.202

Gnomad4 EAS

AF:

0.393

Gnomad4 SAS

AF:

0.320

Gnomad4 FIN

AF:

0.227

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.251

Alfa

AF:

0.106

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 06, 2013	346-19_346-14del in intron 3 of ANKRD1: This variant is not expected to have cli nical significance because it has been identified in 6% (6/100) of control chrom osomes by our laboratory (LMM unpublished data). In addition, this variant lies within a highly variable region of the intron where multiple deletions of variou s sizes identified in the general population have been observed, suggesting that variation in this region is tolerated. -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 17, 2023	- -

Congenital total pulmonary venous return anomaly

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, University Medical Center Utrecht

May 11, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

ANKRD1-related dilated cardiomyopathy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over