3-184233620-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001390846.1(VWA5B2):āc.575T>Gā(p.Leu192Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000574 in 1,551,102 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.575T>G | p.Leu192Arg | missense_variant | 5/20 | ENST00000691901.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VWA5B2 | ENST00000691901.1 | c.575T>G | p.Leu192Arg | missense_variant | 5/20 | NM_001390846.1 | P1 | ||
VWA5B2 | ENST00000426955.6 | c.575T>G | p.Leu192Arg | missense_variant | 4/19 | 1 | P1 | ||
VWA5B2 | ENST00000273794.5 | c.-83T>G | 5_prime_UTR_variant | 2/17 | 2 | ||||
VWA5B2 | ENST00000497229.1 | n.1021T>G | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000151 AC: 23AN: 152384Hom.: 0 AF XY: 0.000173 AC XY: 14AN XY: 81018
GnomAD4 exome AF: 0.0000586 AC: 82AN: 1398924Hom.: 1 Cov.: 33 AF XY: 0.0000783 AC XY: 54AN XY: 689990
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.575T>G (p.L192R) alteration is located in exon 4 (coding exon 4) of the VWA5B2 gene. This alteration results from a T to G substitution at nucleotide position 575, causing the leucine (L) at amino acid position 192 to be replaced by an arginine (R). 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