chr17-4932696-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM1BP4_StrongBS2
The NM_000173.7(GP1BA):c.92T>C(p.Val31Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000862 in 1,613,460 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V31E) has been classified as Uncertain significance.
Frequency
Consequence
NM_000173.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GP1BA | NM_000173.7 | c.92T>C | p.Val31Ala | missense_variant | 2/2 | ENST00000329125.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GP1BA | ENST00000329125.6 | c.92T>C | p.Val31Ala | missense_variant | 2/2 | 1 | NM_000173.7 | P1 | |
CHRNE | ENST00000649830.1 | c.-888+1646A>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000738 AC: 112AN: 151762Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00125 AC: 312AN: 249288Hom.: 2 AF XY: 0.00129 AC XY: 174AN XY: 135228
GnomAD4 exome AF: 0.000874 AC: 1278AN: 1461698Hom.: 6 Cov.: 37 AF XY: 0.000893 AC XY: 649AN XY: 727136
GnomAD4 genome ? AF: 0.000738 AC: 112AN: 151762Hom.: 1 Cov.: 32 AF XY: 0.000540 AC XY: 40AN XY: 74122
ClinVar
Submissions by phenotype
Bernard Soulier syndrome;C1280798:Pseudo von Willebrand disease;C3277076:Bernard-Soulier syndrome, type A2, autosomal dominant Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at