11-61259064-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152718.2(VWCE):c.2479G>A(p.Ala827Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00026 in 1,613,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152718.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000207 AC: 52AN: 250822Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135608
GnomAD4 exome AF: 0.000270 AC: 395AN: 1461676Hom.: 0 Cov.: 31 AF XY: 0.000252 AC XY: 183AN XY: 727124
GnomAD4 genome AF: 0.000164 AC: 25AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2479G>A (p.A827T) alteration is located in exon 20 (coding exon 20) of the VWCE gene. This alteration results from a G to A substitution at nucleotide position 2479, causing the alanine (A) at amino acid position 827 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at