12-55701110-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002206.3(ITGA7):āc.459C>Gā(p.Ile153Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,614,234 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_002206.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.459C>G | p.Ile153Met | missense_variant | 4/25 | ENST00000257879.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA7 | ENST00000257879.11 | c.459C>G | p.Ile153Met | missense_variant | 4/25 | 1 | NM_002206.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00615 AC: 936AN: 152228Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00134 AC: 338AN: 251382Hom.: 1 AF XY: 0.00102 AC XY: 138AN XY: 135884
GnomAD4 exome AF: 0.000592 AC: 865AN: 1461888Hom.: 10 Cov.: 32 AF XY: 0.000517 AC XY: 376AN XY: 727248
GnomAD4 genome AF: 0.00616 AC: 939AN: 152346Hom.: 8 Cov.: 33 AF XY: 0.00609 AC XY: 454AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 24, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 03, 2017 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
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 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at