10-90915892-GAA-GA

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_014391.3(ANKRD1):c.652-13delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,611,048 control chromosomes in the GnomAD database, including 20,419 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2332 hom., cov: 25)

Exomes 𝑓: 0.16 ( 18087 hom. )

Consequence

ANKRD1
NM_014391.3 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 2.87

Publications

6 publications found

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 Gene-Disease associations (from GenCC):

familial isolated dilated cardiomyopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
dilated cardiomyopathy
Inheritance: AD Classification: LIMITED Submitted by: ClinGen
hypertrophic cardiomyopathy
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ANKRD1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 10-90915892-GA-G is Benign according to our data. Variant chr10-90915892-GA-G is described in ClinVar as [Likely_benign]. Clinvar id is 201661.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD1	NM_014391.3 link	c.652-13delT		intron_variant	Intron 6 of 8	ENST00000371697.4	NP_055206.2	Q15327A0A384NYH5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD1	ENST00000371697.4 link	c.652-13delT		intron_variant	Intron 6 of 8	1	NM_014391.3	ENSP00000360762.3		Q15327

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26111

AN:

151198

Hom.:

2326

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.0474

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.156

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.156

Gnomad NFE

AF:

0.162

Gnomad OTH

AF:

0.133

GnomAD2 exomes

AF:

0.150

AC:

37486

AN:

249262

AF XY:

0.151

show subpopulations

Gnomad AFR exome

AF:

0.230

Gnomad AMR exome

AF:

0.113

Gnomad ASJ exome

AF:

0.101

Gnomad EAS exome

AF:

0.153

Gnomad FIN exome

AF:

0.150

Gnomad NFE exome

AF:

0.159

Gnomad OTH exome

AF:

0.144

GnomAD4 exome

AF:

0.155

AC:

226340

AN:

1459732

Hom.:

18087

Cov.:

AF XY:

0.155

AC XY:

112313

AN XY:

726162

show subpopulations

African (AFR)

AF:

0.230

AC:

7693

AN:

33408

American (AMR)

AF:

0.115

AC:

5155

AN:

44690

Ashkenazi Jewish (ASJ)

AF:

0.105

AC:

2738

AN:

26128

East Asian (EAS)

AF:

0.160

AC:

6336

AN:

39622

South Asian (SAS)

AF:

0.139

AC:

11987

AN:

86108

European-Finnish (FIN)

AF:

0.151

AC:

8079

AN:

53348

Middle Eastern (MID)

AF:

0.101

AC:

488

AN:

4836

European-Non Finnish (NFE)

AF:

0.157

AC:

174801

AN:

1111332

Other (OTH)

AF:

0.150

AC:

9063

AN:

60260

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

10299

20597

30896

41194

51493

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.173

AC:

26145

AN:

151316

Hom.:

2332

Cov.:

AF XY:

0.171

AC XY:

12627

AN XY:

73900

show subpopulations

African (AFR)

AF:

0.225

AC:

9236

AN:

41140

American (AMR)

AF:

0.140

AC:

2126

AN:

15220

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

386

AN:

3462

East Asian (EAS)

AF:

0.156

AC:

799

AN:

5118

South Asian (SAS)

AF:

0.138

AC:

653

AN:

4746

European-Finnish (FIN)

AF:

0.150

AC:

1566

AN:

10472

Middle Eastern (MID)

AF:

0.151

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.162

AC:

11011

AN:

67860

Other (OTH)

AF:

0.134

AC:

281

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1005

2010

3016

4021

5026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.166

Hom.:

383

Bravo

AF:

0.172

Asia WGS

AF:

0.159

AC:

554

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 10, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jul 31, 2017

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant summary: The ANKRD1 c.652-13delT variant involves the alteration of a non-conserved intronic nucleotide. Mutation taster predicts a benign outcome for this variant. 3/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 18376/112060 control chromosomes (1459 homozygotes) from ExAC at a frequency of 0.1639836, which is approximately 4770 times the estimated maximal expected allele frequency of a pathogenic ANKRD1 variant (0.0000344), thus it is a common benign polymorphism. This variant has also been reported as a polymorphism in the literature (Arimura_2009). In addition, multiple clinical diagnostic laboratories/reputable databases have classified this variant as benign/likely benign. Taken together, this variant is classified as benign. -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Dilated Cardiomyopathy, Dominant

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

ANKRD1-related dilated cardiomyopathy

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hypertrophic cardiomyopathy 2

Benign:1

Institute of Human Genetics, University of Wuerzburg

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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

Publications

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10-90915892-GAA-GA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over