3-184233349-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001390846.1(VWA5B2):c.482C>T(p.Pro161Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000779 in 1,539,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001390846.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VWA5B2 | NM_001390846.1 | c.482C>T | p.Pro161Leu | missense_variant | 4/20 | ENST00000691901.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWA5B2 | ENST00000691901.1 | c.482C>T | p.Pro161Leu | missense_variant | 4/20 | NM_001390846.1 | P1 | ||
VWA5B2 | ENST00000426955.6 | c.482C>T | p.Pro161Leu | missense_variant | 3/19 | 1 | P1 | ||
VWA5B2 | ENST00000497229.1 | n.750C>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000146 AC: 2AN: 137268Hom.: 0 AF XY: 0.0000273 AC XY: 2AN XY: 73360
GnomAD4 exome AF: 0.00000721 AC: 10AN: 1387320Hom.: 0 Cov.: 33 AF XY: 0.00000439 AC XY: 3AN XY: 683776
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2024 | The c.482C>T (p.P161L) alteration is located in exon 3 (coding exon 3) of the VWA5B2 gene. This alteration results from a C to T substitution at nucleotide position 482, causing the proline (P) at amino acid position 161 to be replaced by a leucine (L). 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