19-55014288-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001083899.2(GP6):āc.1657A>Gā(p.Asn553Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00007 in 1,414,268 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001083899.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152000Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000582 AC: 14AN: 240518Hom.: 0 AF XY: 0.0000381 AC XY: 5AN XY: 131112
GnomAD4 exome AF: 0.0000689 AC: 87AN: 1262268Hom.: 0 Cov.: 18 AF XY: 0.0000564 AC XY: 36AN XY: 637862
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152000Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74252
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces asparagine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 553 of the GP6 protein (p.Asn553Asp). This variant is present in population databases (rs201681535, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with GP6-related conditions. ClinVar contains an entry for this variant (Variation ID: 2196060). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at