chr12-6011792-G-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_000552.5(VWF):c.5667C>T(p.Pro1889=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00415 in 1,609,390 control chromosomes in the GnomAD database, including 165 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P1889P) has been classified as Uncertain significance.
Frequency
Consequence
NM_000552.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWF | NM_000552.5 | c.5667C>T | p.Pro1889= | splice_region_variant, synonymous_variant | 34/52 | ENST00000261405.10 | |
VWF | XM_047429501.1 | c.5667C>T | p.Pro1889= | splice_region_variant, synonymous_variant | 34/52 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWF | ENST00000261405.10 | c.5667C>T | p.Pro1889= | splice_region_variant, synonymous_variant | 34/52 | 1 | NM_000552.5 | P1 | |
VWF | ENST00000538635.5 | n.421-17858C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0195 AC: 2963AN: 151846Hom.: 77 Cov.: 31
GnomAD3 exomes AF: 0.00531 AC: 1231AN: 231986Hom.: 29 AF XY: 0.00409 AC XY: 517AN XY: 126550
GnomAD4 exome AF: 0.00255 AC: 3722AN: 1457426Hom.: 89 Cov.: 29 AF XY: 0.00224 AC XY: 1627AN XY: 725284
GnomAD4 genome AF: 0.0195 AC: 2965AN: 151964Hom.: 76 Cov.: 31 AF XY: 0.0187 AC XY: 1388AN XY: 74250
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
von Willebrand disease type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
von Willebrand disease type 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Aug 09, 2022 | - - |
von Willebrand disease type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Hereditary von Willebrand disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at