chr12-55685300-C-G

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.3184-12G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 1,612,502 control chromosomes in the GnomAD database, including 231,849 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 19996 hom., cov: 33)

Exomes 𝑓: 0.53 ( 211853 hom. )

Consequence

ITGA7
NM_002206.3 intron

Scores

Splicing: ADA: 0.00005187

Clinical Significance

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

Conservation

PhyloP100: -0.736

Publications

13 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=-0.82).

BP6

Variant 12-55685300-C-G is Benign according to our data. Variant chr12-55685300-C-G is described in ClinVar as Benign. ClinVar VariationId is 94043.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.3184-12G>C		intron_variant	Intron 24 of 24	ENST00000257879.11	NP_002197.2	Q13683-7Q4LE35

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA7	ENST00000257879.11 link	c.3184-12G>C		intron_variant	Intron 24 of 24	1	NM_002206.3	ENSP00000257879.7		Q13683-7

Frequencies

GnomAD3 genomes

AF:

0.491

AC:

74629

AN:

152044

Hom.:

19985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.299

Gnomad AMI

AF:

0.572

Gnomad AMR

AF:

0.602

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.935

Gnomad SAS

AF:

0.726

Gnomad FIN

AF:

0.651

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.476

GnomAD2 exomes

AF:

0.591

AC:

148000

AN:

250454

AF XY:

0.593

show subpopulations

Gnomad AFR exome

AF:

0.293

Gnomad AMR exome

AF:

0.714

Gnomad ASJ exome

AF:

0.460

Gnomad EAS exome

AF:

0.939

Gnomad FIN exome

AF:

0.650

Gnomad NFE exome

AF:

0.511

Gnomad OTH exome

AF:

0.549

GnomAD4 exome

AF:

0.528

AC:

771012

AN:

1460340

Hom.:

211853

Cov.:

AF XY:

0.533

AC XY:

387447

AN XY:

726536

show subpopulations

African (AFR)

AF:

0.283

AC:

9475

AN:

33456

American (AMR)

AF:

0.701

AC:

31331

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.464

AC:

12131

AN:

26134

East Asian (EAS)

AF:

0.935

AC:

37106

AN:

39698

South Asian (SAS)

AF:

0.703

AC:

60598

AN:

86232

European-Finnish (FIN)

AF:

0.640

AC:

33842

AN:

52900

Middle Eastern (MID)

AF:

0.500

AC:

2885

AN:

5766

European-Non Finnish (NFE)

AF:

0.497

AC:

551740

AN:

1111088

Other (OTH)

AF:

0.529

AC:

31904

AN:

60354

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

17181

34362

51544

68725

85906

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16130

32260

48390

64520

80650

<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:

0.491

AC:

74667

AN:

152162

Hom.:

19996

Cov.:

AF XY:

0.506

AC XY:

37614

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.299

AC:

12417

AN:

41526

American (AMR)

AF:

0.602

AC:

9218

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.459

AC:

1592

AN:

3470

East Asian (EAS)

AF:

0.935

AC:

4823

AN:

5156

South Asian (SAS)

AF:

0.724

AC:

3493

AN:

4826

European-Finnish (FIN)

AF:

0.651

AC:

6901

AN:

10604

Middle Eastern (MID)

AF:

0.490

AC:

144

AN:

294

European-Non Finnish (NFE)

AF:

0.508

AC:

34543

AN:

67960

Other (OTH)

AF:

0.480

AC:

1014

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1867

3733

5600

7466

9333

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

672

1344

2016

2688

3360

<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:

0.487

Hom.:

3354

Bravo

AF:

0.474

Asia WGS

AF:

0.770

AC:

2674

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

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

- -

Jan 22, 2016

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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. -

Congenital muscular dystrophy due to integrin alpha-7 deficiency

Benign:2

Aug 19, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.3

(source)

DANN

Benign

0.65

PhyloP100

-0.74

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000052

dbscSNV1_RF

Benign

0.038

SpliceAI score (max)

0.010

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