chr7-12351649-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001135924.3(VWDE):āc.3810T>Gā(p.Ser1270Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,398,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.3810T>G | p.Ser1270Arg | missense_variant | 19/29 | ENST00000275358.8 | |
VWDE | NM_001346972.2 | c.3465T>G | p.Ser1155Arg | missense_variant | 17/27 | ||
VWDE | NM_001346973.2 | c.3000T>G | p.Ser1000Arg | missense_variant | 17/27 | ||
VWDE | NR_144534.2 | n.4632T>G | non_coding_transcript_exon_variant | 20/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWDE | ENST00000275358.8 | c.3810T>G | p.Ser1270Arg | missense_variant | 19/29 | 5 | NM_001135924.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000642 AC: 1AN: 155836Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82550
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1398164Hom.: 0 Cov.: 31 AF XY: 0.00000290 AC XY: 2AN XY: 689540
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2023 | The c.3810T>G (p.S1270R) alteration is located in exon 19 (coding exon 19) of the VWDE gene. This alteration results from a T to G substitution at nucleotide position 3810, causing the serine (S) at amino acid position 1270 to be replaced by an arginine (R). 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