rs7971022
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002206.3(ITGA7):āc.1965T>Cā(p.Cys655Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0208 in 1,612,240 control chromosomes in the GnomAD database, including 431 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.014 ( 29 hom., cov: 30)
Exomes š: 0.021 ( 402 hom. )
Consequence
ITGA7
NM_002206.3 synonymous
NM_002206.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.04
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 -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 12-55695560-A-G is Benign according to our data. Variant chr12-55695560-A-G is described in ClinVar as [Benign]. Clinvar id is 94036.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-55695560-A-G is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=-1.04 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0144 (2168/150850) while in subpopulation NFE AF= 0.0235 (1592/67778). AF 95% confidence interval is 0.0225. There are 29 homozygotes in gnomad4. There are 1012 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 29 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGA7 | NM_002206.3 | c.1965T>C | p.Cys655Cys | synonymous_variant | 14/25 | ENST00000257879.11 | NP_002197.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGA7 | ENST00000257879.11 | c.1965T>C | p.Cys655Cys | synonymous_variant | 14/25 | 1 | NM_002206.3 | ENSP00000257879.7 |
Frequencies
GnomAD3 genomes AF: 0.0144 AC: 2166AN: 150736Hom.: 29 Cov.: 30
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GnomAD3 exomes AF: 0.0162 AC: 4066AN: 251454Hom.: 45 AF XY: 0.0171 AC XY: 2330AN XY: 135908
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GnomAD4 exome AF: 0.0214 AC: 31306AN: 1461390Hom.: 402 Cov.: 33 AF XY: 0.0215 AC XY: 15596AN XY: 727030
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GnomAD4 genome AF: 0.0144 AC: 2168AN: 150850Hom.: 29 Cov.: 30 AF XY: 0.0137 AC XY: 1012AN XY: 73666
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ClinVar
Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:5
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 29, 2016 | 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. - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 31, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 10, 2013 | - - |
Congenital muscular dystrophy due to integrin alpha-7 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at