rs17138632
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173800.5(LVRN):c.1918G>A(p.Val640Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,425,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 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. V640F) has been classified as Likely benign.
Frequency
Consequence
NM_173800.5 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 |
---|---|---|---|---|---|---|---|
LVRN | NM_173800.5 | c.1918G>A | p.Val640Ile | missense_variant | 12/20 | ENST00000357872.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LVRN | ENST00000357872.9 | c.1918G>A | p.Val640Ile | missense_variant | 12/20 | 1 | NM_173800.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000444 AC: 1AN: 225430Hom.: 0 AF XY: 0.00000816 AC XY: 1AN XY: 122600
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1425776Hom.: 0 Cov.: 30 AF XY: 0.00000141 AC XY: 1AN XY: 709610
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at