chr3-124796651-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002213.5(ITGB5):āc.1430A>Gā(p.Asn477Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0369 in 1,613,950 control chromosomes in the GnomAD database, including 1,516 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002213.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB5 | NM_002213.5 | c.1430A>G | p.Asn477Ser | missense_variant | 10/15 | ENST00000296181.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB5 | ENST00000296181.9 | c.1430A>G | p.Asn477Ser | missense_variant | 10/15 | 1 | NM_002213.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0481 AC: 7325AN: 152164Hom.: 252 Cov.: 33
GnomAD3 exomes AF: 0.0436 AC: 10911AN: 250414Hom.: 342 AF XY: 0.0452 AC XY: 6121AN XY: 135556
GnomAD4 exome AF: 0.0358 AC: 52289AN: 1461668Hom.: 1262 Cov.: 35 AF XY: 0.0371 AC XY: 26999AN XY: 727148
GnomAD4 genome AF: 0.0482 AC: 7345AN: 152282Hom.: 254 Cov.: 33 AF XY: 0.0478 AC XY: 3562AN XY: 74456
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at