17-44372421-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_000419.5(ITGA2B):c.3063C>A(p.Val1021=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. V1021V) has been classified as Benign.
Frequency
Consequence
NM_000419.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA2B | NM_000419.5 | c.3063C>A | p.Val1021= | splice_region_variant, synonymous_variant | 30/30 | ENST00000262407.6 | |
ITGA2B | XM_011524749.2 | c.3114C>A | p.Val1038= | splice_region_variant, synonymous_variant | 29/29 | ||
ITGA2B | XM_011524750.2 | c.3099C>A | p.Val1033= | splice_region_variant, synonymous_variant | 29/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA2B | ENST00000262407.6 | c.3063C>A | p.Val1021= | splice_region_variant, synonymous_variant | 30/30 | 1 | NM_000419.5 | P1 | |
ITGA2B | ENST00000648408.1 | c.2379C>A | p.Val793= | splice_region_variant, synonymous_variant | 25/25 | ||||
ITGA2B | ENST00000587295.5 | c.258C>A | p.Val86= | splice_region_variant, synonymous_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.84e-7 AC: 1AN: 1461620Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0AN XY: 727122
GnomAD4 genome ? Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at