chr12-55694989-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -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

Publications

17 publications found

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 Gene-Disease associations (from GenCC):

congenital muscular dystrophy due to integrin alpha-7 deficiency
Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet
congenital fiber-type disproportion myopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ITGA7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 94037.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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 rank	MANE	Protein	UniProt
ITGA7	NM_002206.3 link	c.2004-19G>A		intron_variant	Intron 14 of 24	ENST00000257879.11	NP_002197.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA7	ENST00000257879.11 link	c.2004-19G>A		intron_variant	Intron 14 of 24	1	NM_002206.3	ENSP00000257879.7

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

GnomAD2 exomes

AF:

0.592

AC:

142508

AN:

240686

AF XY:

0.593

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 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

African (AFR)

AF:

0.277

AC:

9280

AN:

33460

American (AMR)

AF:

0.700

AC:

31189

AN:

44576

Ashkenazi Jewish (ASJ)

AF:

0.460

AC:

12028

AN:

26124

East Asian (EAS)

AF:

0.934

AC:

37073

AN:

39672

South Asian (SAS)

AF:

0.692

AC:

59650

AN:

86162

European-Finnish (FIN)

AF:

0.641

AC:

32360

AN:

50508

Middle Eastern (MID)

AF:

0.498

AC:

2871

AN:

5766

European-Non Finnish (NFE)

AF:

0.498

AC:

553685

AN:

1110770

Other (OTH)

AF:

0.528

AC:

31829

AN:

60298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

18447

36895

55342

73790

92237

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16162

32324

48486

64648

80810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.489

AC:

74251

AN:

151858

Hom.:

19847

Cov.:

AF XY:

0.503

AC XY:

37331

AN XY:

74220

show subpopulations

African (AFR)

AF:

0.294

AC:

12158

AN:

41416

American (AMR)

AF:

0.596

AC:

9117

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.454

AC:

1573

AN:

3464

East Asian (EAS)

AF:

0.935

AC:

4800

AN:

5134

South Asian (SAS)

AF:

0.715

AC:

3437

AN:

4810

European-Finnish (FIN)

AF:

0.652

AC:

6887

AN:

10570

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.510

AC:

34608

AN:

67866

Other (OTH)

AF:

0.478

AC:

1007

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1746

3491

5237

6982

8728

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

666

1332

1998

2664

3330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.478

Hom.:

3792

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

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Jul 18, 2012

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Congenital muscular dystrophy due to integrin alpha-7 deficiency

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Aug 19, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Mar 03, 2015

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.5

(source)

DANN

Benign

0.62

PhyloP100

0.082

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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