10-70301415-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001278212.2(LRRC20):c.494C>T(p.Pro165Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001278212.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC20 | NM_001278212.2 | c.494C>T | p.Pro165Leu | missense_variant | 5/5 | ENST00000446961.4 | NP_001265141.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC20 | ENST00000446961.4 | c.494C>T | p.Pro165Leu | missense_variant | 5/5 | 2 | NM_001278212.2 | ENSP00000413745.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250292Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135404
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461450Hom.: 0 Cov.: 34 AF XY: 0.00000963 AC XY: 7AN XY: 727042
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152366Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74520
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.494C>T (p.P165L) alteration is located in exon 5 (coding exon 4) of the LRRC20 gene. This alteration results from a C to T substitution at nucleotide position 494, causing the proline (P) at amino acid position 165 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