12-55698805-G-A
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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):c.903C>T(p.Ser301=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,614,112 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0065 ( 10 hom., cov: 32)
Exomes 𝑓: 0.00068 ( 13 hom. )
Consequence
ITGA7
NM_002206.3 synonymous
NM_002206.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.22
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=-0.54).
BP6
Variant 12-55698805-G-A is Benign according to our data. Variant chr12-55698805-G-A is described in ClinVar as [Benign]. Clinvar id is 309795.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.22 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00646 (984/152290) while in subpopulation AFR AF= 0.0227 (944/41556). AF 95% confidence interval is 0.0215. There are 10 homozygotes in gnomad4. There are 484 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA7 | NM_002206.3 | c.903C>T | p.Ser301= | synonymous_variant | 6/25 | ENST00000257879.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA7 | ENST00000257879.11 | c.903C>T | p.Ser301= | synonymous_variant | 6/25 | 1 | NM_002206.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00644 AC: 980AN: 152172Hom.: 10 Cov.: 32
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GnomAD3 exomes AF: 0.00183 AC: 460AN: 250928Hom.: 5 AF XY: 0.00133 AC XY: 181AN XY: 135776
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GnomAD4 exome AF: 0.000678 AC: 991AN: 1461822Hom.: 13 Cov.: 33 AF XY: 0.000554 AC XY: 403AN XY: 727224
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GnomAD4 genome AF: 0.00646 AC: 984AN: 152290Hom.: 10 Cov.: 32 AF XY: 0.00650 AC XY: 484AN XY: 74464
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 06, 2017 | 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:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
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BayesDel_noAF
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at