rs72609545
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_016379.4(VCX3A):c.418G>T(p.Val140Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V140M) has been classified as Benign.
Frequency
Consequence
NM_016379.4 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 |
---|---|---|---|---|---|---|---|
VCX3A | NM_016379.4 | c.418G>T | p.Val140Leu | missense_variant | 3/3 | ENST00000381089.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCX3A | ENST00000381089.7 | c.418G>T | p.Val140Leu | missense_variant | 3/3 | 1 | NM_016379.4 | P2 | |
VCX3A | ENST00000398729.1 | c.358G>T | p.Val120Leu | missense_variant, splice_region_variant | 4/4 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 13
GnomAD4 exome AF: 0.0000536 AC: 21AN: 392037Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0AN XY: 151489
GnomAD4 genome ? Cov.: 13
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.