rs121909750
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_000407.5(GP1BB):āc.338A>Gā(p.Tyr113Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000451 in 1,108,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y113F) has been classified as Uncertain significance.
Frequency
Consequence
NM_000407.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GP1BB | NM_000407.5 | c.338A>G | p.Tyr113Cys | missense_variant | 2/2 | ENST00000366425.4 | |
SEPT5-GP1BB | NR_037611.1 | n.4078A>G | non_coding_transcript_exon_variant | 12/12 | |||
SEPT5-GP1BB | NR_037612.1 | n.2582A>G | non_coding_transcript_exon_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GP1BB | ENST00000366425.4 | c.338A>G | p.Tyr113Cys | missense_variant | 2/2 | 1 | NM_000407.5 | P1 | |
SEPTIN5 | ENST00000470814.1 | n.2310A>G | non_coding_transcript_exon_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000451 AC: 5AN: 1108830Hom.: 0 Cov.: 31 AF XY: 0.00000562 AC XY: 3AN XY: 534278
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Macrothrombocytopenia, familial, Bernard-Soulier type Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 1997 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at