rs61733050
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002206.3(ITGA7):c.1609C>T(p.Arg537Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,613,996 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R537Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_002206.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA7 | NM_002206.3 | c.1609C>T | p.Arg537Trp | missense_variant | 12/25 | ENST00000257879.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA7 | ENST00000257879.11 | c.1609C>T | p.Arg537Trp | missense_variant | 12/25 | 1 | NM_002206.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00570 AC: 868AN: 152158Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00153 AC: 383AN: 251066Hom.: 4 AF XY: 0.00108 AC XY: 147AN XY: 135730
GnomAD4 exome AF: 0.000601 AC: 879AN: 1461720Hom.: 14 Cov.: 33 AF XY: 0.000527 AC XY: 383AN XY: 727150
GnomAD4 genome AF: 0.00570 AC: 868AN: 152276Hom.: 8 Cov.: 33 AF XY: 0.00559 AC XY: 416AN XY: 74450
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 13, 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. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Congenital muscular dystrophy due to integrin alpha-7 deficiency Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 23, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 25, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 24, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at