chr17-44379780-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_000419.5(ITGA2B):c.1787T>A(p.Ile596Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I596T) has been classified as Pathogenic.
Frequency
Consequence
NM_000419.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA2B | NM_000419.5 | c.1787T>A | p.Ile596Asn | missense_variant | 18/30 | ENST00000262407.6 | |
ITGA2B | XM_011524749.2 | c.1940T>A | p.Ile647Asn | missense_variant | 18/29 | ||
ITGA2B | XM_011524750.2 | c.1940T>A | p.Ile647Asn | missense_variant | 18/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA2B | ENST00000262407.6 | c.1787T>A | p.Ile596Asn | missense_variant | 18/30 | 1 | NM_000419.5 | P1 | |
ITGA2B | ENST00000648408.1 | c.1220T>A | p.Ile407Asn | missense_variant | 14/25 | ||||
ITGA2B | ENST00000592462.5 | n.582T>A | non_coding_transcript_exon_variant | 7/15 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at