12-55694989-C-T

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

2

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]

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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
ITGA7NM_002206.3 linkc.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
ITGA7ENST00000257879.11 linkc.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.:
30
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.:
36
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.:
30
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 submitterclinical testingEurofins Ntd Llc (ga)Jul 18, 2012- -
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Congenital muscular dystrophy due to integrin alpha-7 deficiency Benign:2
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabAug 19, 2021- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxMar 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.

Other links and lift over

dbSNP: rs2293410; hg19: chr12-56088773; API