12-6019004-C-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_000552.5(VWF):c.4414G>T(p.Asp1472Tyr) 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 1,613,460 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1472P?) has been classified as Uncertain significance.
Frequency
Consequence
NM_000552.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWF | NM_000552.5 | c.4414G>T | p.Asp1472Tyr | missense_variant | 28/52 | ENST00000261405.10 | |
VWF | XM_047429501.1 | c.4414G>T | p.Asp1472Tyr | missense_variant | 28/52 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWF | ENST00000261405.10 | c.4414G>T | p.Asp1472Tyr | missense_variant | 28/52 | 1 | NM_000552.5 | P1 | |
VWF | ENST00000538635.5 | n.421-25070G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00158 AC: 240AN: 151904Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000266 AC: 66AN: 248378Hom.: 0 AF XY: 0.000178 AC XY: 24AN XY: 134782
GnomAD4 exome AF: 0.000119 AC: 174AN: 1461438Hom.: 0 Cov.: 99 AF XY: 0.000103 AC XY: 75AN XY: 727008
GnomAD4 genome ? AF: 0.00161 AC: 245AN: 152022Hom.: 1 Cov.: 31 AF XY: 0.00163 AC XY: 121AN XY: 74306
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at