chr7-12356207-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001135924.3(VWDE):c.3649G>T(p.Val1217Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000214 in 1,399,364 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001135924.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWDE | NM_001135924.3 | c.3649G>T | p.Val1217Leu | missense_variant | 18/29 | ENST00000275358.8 | |
VWDE | NM_001346972.2 | c.3304G>T | p.Val1102Leu | missense_variant | 16/27 | ||
VWDE | NM_001346973.2 | c.2839G>T | p.Val947Leu | missense_variant | 16/27 | ||
VWDE | NR_144534.2 | n.3798G>T | non_coding_transcript_exon_variant | 18/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWDE | ENST00000275358.8 | c.3649G>T | p.Val1217Leu | missense_variant | 18/29 | 5 | NM_001135924.3 | P1 | |
VWDE | ENST00000452576.6 | c.3649G>T | p.Val1217Leu | missense_variant, NMD_transcript_variant | 18/30 | 1 | |||
VWDE | ENST00000644150.1 | c.124G>T | p.Val42Leu | missense_variant | 1/3 | ||||
VWDE | ENST00000521169.5 | c.*2027G>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/26 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000639 AC: 1AN: 156538Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82972
GnomAD4 exome AF: 0.00000214 AC: 3AN: 1399364Hom.: 0 Cov.: 35 AF XY: 0.00000290 AC XY: 2AN XY: 690188
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.3649G>T (p.V1217L) alteration is located in exon 18 (coding exon 18) of the VWDE gene. This alteration results from a G to T substitution at nucleotide position 3649, causing the valine (V) at amino acid position 1217 to be replaced by a leucine (L). 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