Variant chr6-144291828-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The NM_007124.3(UTRN):c.-1G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00818 in 1,610,884 control chromosomes in the GnomAD database, including 844 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.013 ( 87 hom., cov: 33)

Exomes 𝑓: 0.0076 ( 757 hom. )

Consequence

UTRN
NM_007124.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.897

Variant links:

Genes affected

UTRN (HGNC:12635): (utrophin) This gene shares both structural and functional similarities with the dystrophin gene. It contains an actin-binding N-terminus, a triple coiled-coil repeat central region, and a C-terminus that consists of protein-protein interaction motifs which interact with dystroglycan protein components. The protein encoded by this gene is located at the neuromuscular synapse and myotendinous junctions, where it participates in post-synaptic membrane maintenance and acetylcholine receptor clustering. Mouse studies suggest that this gene may serve as a functional substitute for the dystrophin gene and therefore, may serve as a potential therapeutic alternative to muscular dystrophy which is caused by mutations in the dystrophin gene. Alternative splicing of the utrophin gene has been described; however, the full-length nature of these variants has not yet been determined. [provided by RefSeq, Jul 2008]

UTRN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 6-144291828-G-A is Benign according to our data. Variant chr6-144291828-G-A is described in ClinVar as [Benign]. Clinvar id is 1275590.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTRN	NM_007124.3 linkuse as main transcript	c.-1G>A		5_prime_UTR_variant	2/75	ENST00000367545.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UTRN	ENST00000367545.8 linkuse as main transcript	c.-1G>A		5_prime_UTR_variant	2/75	5	NM_007124.3	P1	P46939-1

Frequencies

GnomAD3 genomes

AF:

0.0134

AC:

2039

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0177

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0133

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.162

Gnomad SAS

AF:

0.0118

Gnomad FIN

AF:

0.0106

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000852

Gnomad OTH

AF:

0.0119

GnomAD3 exomes

AF:

0.0188

AC:

4672

AN:

248124

Hom.:

251

AF XY:

0.0167

AC XY:

2240

AN XY:

134060

show subpopulations

Gnomad AFR exome

AF:

0.0181

Gnomad AMR exome

AF:

0.0319

Gnomad ASJ exome

AF:

0.00161

Gnomad EAS exome

AF:

0.154

Gnomad SAS exome

AF:

0.00464

Gnomad FIN exome

AF:

0.00930

Gnomad NFE exome

AF:

0.000825

Gnomad OTH exome

AF:

0.0114

GnomAD4 exome

AF:

0.00764

AC:

11143

AN:

1458540

Hom.:

757

Cov.:

AF XY:

0.00741

AC XY:

5379

AN XY:

725460

show subpopulations

Gnomad4 AFR exome

AF:

0.0167

Gnomad4 AMR exome

AF:

0.0286

Gnomad4 ASJ exome

AF:

0.000961

Gnomad4 EAS exome

AF:

0.186

Gnomad4 SAS exome

AF:

0.00589

Gnomad4 FIN exome

AF:

0.00941

Gnomad4 NFE exome

AF:

0.000338

Gnomad4 OTH exome

AF:

0.00933

GnomAD4 genome

AF:

0.0134

AC:

2038

AN:

152344

Hom.:

Cov.:

AF XY:

0.0145

AC XY:

1083

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.0177

Gnomad4 AMR

AF:

0.0133

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.162

Gnomad4 SAS

AF:

0.0118

Gnomad4 FIN

AF:

0.0106

Gnomad4 NFE

AF:

0.000852

Gnomad4 OTH

AF:

0.0113

Alfa

AF:

0.00427

Hom.:

Bravo

AF:

0.0153

Asia WGS

AF:

0.0580

AC:

201

AN:

3478

EpiCase

AF:

0.000437

EpiControl

AF:

0.000297

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 09, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

0.86

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