chr12-6011792-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_000552.5(VWF):āc.5667C>Gā(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 0.00000658 in 151,866 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. P1889P) has been classified as Likely benign.
Frequency
Consequence
NM_000552.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWF | NM_000552.5 | c.5667C>G | p.Pro1889= | splice_region_variant, synonymous_variant | 34/52 | ENST00000261405.10 | |
VWF | XM_047429501.1 | c.5667C>G | 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>G | p.Pro1889= | splice_region_variant, synonymous_variant | 34/52 | 1 | NM_000552.5 | P1 | |
VWF | ENST00000538635.5 | n.421-17858C>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151866Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000431 AC: 1AN: 231986Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 126550
GnomAD4 exome Cov.: 29
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151866Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74138
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Apr 17, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at