chr13-41732106-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015058.2(VWA8):c.2476C>T(p.Leu826Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000552 in 1,613,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015058.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWA8 | NM_015058.2 | c.2476C>T | p.Leu826Phe | missense_variant | 22/45 | ENST00000379310.8 | |
VWA8 | NM_001009814.2 | c.2476C>T | p.Leu826Phe | missense_variant | 22/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWA8 | ENST00000379310.8 | c.2476C>T | p.Leu826Phe | missense_variant | 22/45 | 2 | NM_015058.2 | P1 | |
VWA8 | ENST00000281496.6 | c.2476C>T | p.Leu826Phe | missense_variant | 22/26 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250930Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135642
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1460986Hom.: 0 Cov.: 30 AF XY: 0.0000702 AC XY: 51AN XY: 726802
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.2476C>T (p.L826F) alteration is located in exon 22 (coding exon 22) of the VWA8 gene. This alteration results from a C to T substitution at nucleotide position 2476, causing the leucine (L) at amino acid position 826 to be replaced by a phenylalanine (F). 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