chr3-184233341-G-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001390846.1(VWA5B2):c.474G>T(p.Pro158=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000911 in 1,536,348 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000087 ( 0 hom. )
Consequence
VWA5B2
NM_001390846.1 synonymous
NM_001390846.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.51
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 3-184233341-G-T is Benign according to our data. Variant chr3-184233341-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2654310.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.51 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWA5B2 | NM_001390846.1 | c.474G>T | p.Pro158= | synonymous_variant | 4/20 | ENST00000691901.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWA5B2 | ENST00000691901.1 | c.474G>T | p.Pro158= | synonymous_variant | 4/20 | NM_001390846.1 | P1 | ||
VWA5B2 | ENST00000426955.6 | c.474G>T | p.Pro158= | synonymous_variant | 3/19 | 1 | P1 | ||
VWA5B2 | ENST00000497229.1 | n.742G>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000752 AC: 1AN: 132932Hom.: 0 AF XY: 0.0000142 AC XY: 1AN XY: 70662
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GnomAD4 exome AF: 0.00000867 AC: 12AN: 1384088Hom.: 0 Cov.: 30 AF XY: 0.0000103 AC XY: 7AN XY: 681788
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74456
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | VWA5B2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at