Variant rs541157 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001386795.1(DTNA):c.1903+17T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 1,613,804 control chromosomes in the GnomAD database, including 13,755 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2251 hom., cov: 32)

Exomes 𝑓: 0.12 ( 11504 hom. )

Consequence

DTNA
NM_001386795.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.00

Variant links:

Genes affected

DTNA (HGNC:3057): (dystrobrevin alpha) The protein encoded by this gene belongs to the dystrobrevin subfamily of the dystrophin family. This protein is a component of the dystrophin-associated protein complex (DPC), which consists of dystrophin and several integral and peripheral membrane proteins, including dystroglycans, sarcoglycans, syntrophins and alpha- and beta-dystrobrevin. The DPC localizes to the sarcolemma and its disruption is associated with various forms of muscular dystrophy. Mutations in this gene are associated with left ventricular noncompaction with congenital heart defects. Multiple alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

DTNA links:

DTNA (HGNC:):

DTNA links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 18-34875415-T-C is Benign according to our data. Variant chr18-34875415-T-C is described in ClinVar as [Benign]. Clinvar id is 137178.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DTNA	NM_001386795.1 linkuse as main transcript	c.1903+17T>C		intron_variant		ENST00000444659.6	NP_001373724.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DTNA	ENST00000444659.6 linkuse as main transcript	c.1903+17T>C		intron_variant		5	NM_001386795.1	ENSP00000405819.2		Q9Y4J8-17A0A7P0TBH9

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24173

AN:

152018

Hom.:

2248

Cov.:

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.0725

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.0100

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.140

GnomAD3 exomes

AF:

0.119

AC:

29765

AN:

250264

Hom.:

2245

AF XY:

0.121

AC XY:

16385

AN XY:

135502

show subpopulations

Gnomad AFR exome

AF:

0.270

Gnomad AMR exome

AF:

0.0610

Gnomad ASJ exome

AF:

0.120

Gnomad EAS exome

AF:

0.0139

Gnomad SAS exome

AF:

0.131

Gnomad FIN exome

AF:

0.158

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.111

GnomAD4 exome

AF:

0.120

AC:

175307

AN:

1461668

Hom.:

11504

Cov.:

AF XY:

0.121

AC XY:

87706

AN XY:

727124

show subpopulations

Gnomad4 AFR exome

AF:

0.271

Gnomad4 AMR exome

AF:

0.0664

Gnomad4 ASJ exome

AF:

0.116

Gnomad4 EAS exome

AF:

0.00756

Gnomad4 SAS exome

AF:

0.131

Gnomad4 FIN exome

AF:

0.155

Gnomad4 NFE exome

AF:

0.119

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.159

AC:

24202

AN:

152136

Hom.:

2251

Cov.:

AF XY:

0.160

AC XY:

11889

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.264

Gnomad4 AMR

AF:

0.104

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.0100

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.164

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.138

Alfa

AF:

0.130

Hom.:

1016

Bravo

AF:

0.157

Asia WGS

AF:

0.0750

AC:

261

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 08, 2014	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Left ventricular noncompaction 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.8

DANN

Benign

0.52

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