10-32920355-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_002211.4(ITGB1):c.1159G>A(p.Gly387Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000166 in 1,613,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002211.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGB1 | NM_002211.4 | c.1159G>A | p.Gly387Ser | missense_variant | 10/16 | ENST00000302278.8 | NP_002202.2 | |
ITGB1 | NM_033668.2 | c.1159G>A | p.Gly387Ser | missense_variant | 9/16 | NP_391988.1 | ||
ITGB1 | NM_133376.3 | c.1159G>A | p.Gly387Ser | missense_variant | 10/16 | NP_596867.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGB1 | ENST00000302278.8 | c.1159G>A | p.Gly387Ser | missense_variant | 10/16 | 1 | NM_002211.4 | ENSP00000303351 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152064Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000797 AC: 20AN: 250890Hom.: 0 AF XY: 0.0000959 AC XY: 13AN XY: 135596
GnomAD4 exome AF: 0.000177 AC: 258AN: 1461152Hom.: 0 Cov.: 31 AF XY: 0.000180 AC XY: 131AN XY: 726908
GnomAD4 genome AF: 0.0000658 AC: 10AN: 152064Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74270
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at