7-12343093-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.4164G>T(p.Arg1388Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,549,006 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 (★).
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VWDE | NM_001135924.3 | c.4164G>T | p.Arg1388Ser | missense_variant | Exon 22 of 29 | ENST00000275358.8 | NP_001129396.1 | |
VWDE | NM_001346972.2 | c.3819G>T | p.Arg1273Ser | missense_variant | Exon 20 of 27 | NP_001333901.1 | ||
VWDE | NM_001346973.2 | c.3354G>T | p.Arg1118Ser | missense_variant | Exon 20 of 27 | NP_001333902.1 | ||
VWDE | NR_144534.2 | n.4986G>T | non_coding_transcript_exon_variant | Exon 23 of 30 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000193 AC: 3AN: 155694Hom.: 0 AF XY: 0.0000363 AC XY: 3AN XY: 82542
GnomAD4 exome AF: 0.0000508 AC: 71AN: 1396898Hom.: 0 Cov.: 30 AF XY: 0.0000537 AC XY: 37AN XY: 689006
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4164G>T (p.R1388S) alteration is located in exon 22 (coding exon 22) of the VWDE gene. This alteration results from a G to T substitution at nucleotide position 4164, causing the arginine (R) at amino acid position 1388 to be replaced by a serine (S). 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