Variant 12-55694989-C-T 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_002206.3(ITGA7):c.2004-19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 1,609,194 control chromosomes in the GnomAD database, including 231,376 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 19847 hom., cov: 30)

Exomes 𝑓: 0.53 ( 211529 hom. )

Consequence

ITGA7
NM_002206.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0820

Variant links:

Genes affected

ITGA7 (HGNC:6143): (integrin subunit alpha 7) The protein encoded by this gene belongs to the integrin alpha chain family. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. They mediate a wide spectrum of cell-cell and cell-matrix interactions, and thus play a role in cell migration, morphologic development, differentiation, and metastasis. This protein functions as a receptor for the basement membrane protein laminin-1. It is mainly expressed in skeletal and cardiac muscles and may be involved in differentiation and migration processes during myogenesis. Defects in this gene are associated with congenital myopathy. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Feb 2009]

ITGA7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 12-55694989-C-T is Benign according to our data. Variant chr12-55694989-C-T is described in ClinVar as [Benign]. Clinvar id is 94037.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-55694989-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGA7	NM_002206.3 link	c.2004-19G>A		intron_variant		ENST00000257879.11	NP_002197.2	Q13683-7Q4LE35

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA7	ENST00000257879.11 link	c.2004-19G>A		intron_variant		1	NM_002206.3	ENSP00000257879.7		Q13683-7

Frequencies

GnomAD3 genomes

AF:

0.489

AC:

74210

AN:

151740

Hom.:

19835

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.572

Gnomad AMR

AF:

0.596

Gnomad ASJ

AF:

0.454

Gnomad EAS

AF:

0.935

Gnomad SAS

AF:

0.716

Gnomad FIN

AF:

0.652

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.510

Gnomad OTH

AF:

0.474

GnomAD3 exomes

AF:

0.592

AC:

142508

AN:

240686

Hom.:

45006

AF XY:

0.593

AC XY:

77640

AN XY:

130844

show subpopulations

Gnomad AFR exome

AF:

0.289

Gnomad AMR exome

AF:

0.713

Gnomad ASJ exome

AF:

0.456

Gnomad EAS exome

AF:

0.939

Gnomad SAS exome

AF:

0.697

Gnomad FIN exome

AF:

0.651

Gnomad NFE exome

AF:

0.513

Gnomad OTH exome

AF:

0.548

GnomAD4 exome

AF:

0.528

AC:

769965

AN:

1457336

Hom.:

211529

Cov.:

AF XY:

0.533

AC XY:

386661

AN XY:

724982

show subpopulations

Gnomad4 AFR exome

AF:

0.277

Gnomad4 AMR exome

AF:

0.700

Gnomad4 ASJ exome

AF:

0.460

Gnomad4 EAS exome

AF:

0.934

Gnomad4 SAS exome

AF:

0.692

Gnomad4 FIN exome

AF:

0.641

Gnomad4 NFE exome

AF:

0.498

Gnomad4 OTH exome

AF:

0.528

GnomAD4 genome

AF:

0.489

AC:

74251

AN:

151858

Hom.:

19847

Cov.:

AF XY:

0.503

AC XY:

37331

AN XY:

74220

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.596

Gnomad4 ASJ

AF:

0.454

Gnomad4 EAS

AF:

0.935

Gnomad4 SAS

AF:

0.715

Gnomad4 FIN

AF:

0.652

Gnomad4 NFE

AF:

0.510

Gnomad4 OTH

AF:

0.478

Alfa

AF:

0.483

Hom.:

3754

Bravo

AF:

0.473

Asia WGS

AF:

0.767

AC:

2666

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 18, 2012	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Congenital muscular dystrophy due to integrin alpha-7 deficiency

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Aug 19, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.5

DANN

Benign

0.62

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

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