rs1445708
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_173800.5(LVRN):c.663C>A(p.Phe221Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,566 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_173800.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LVRN | NM_173800.5 | c.663C>A | p.Phe221Leu | missense_variant | 1/20 | ENST00000357872.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LVRN | ENST00000357872.9 | c.663C>A | p.Phe221Leu | missense_variant | 1/20 | 1 | NM_173800.5 | P1 | |
LVRN | ENST00000504467.5 | c.663C>A | p.Phe221Leu | missense_variant, NMD_transcript_variant | 1/20 | 1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000418 AC: 1AN: 239172Hom.: 0 AF XY: 0.00000764 AC XY: 1AN XY: 130846
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459566Hom.: 0 Cov.: 53 AF XY: 0.00000138 AC XY: 1AN XY: 725958
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at