rs141782332
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_001040616.3(LINS1):c.52G>A(p.Gly18Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000384 in 1,610,368 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001040616.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00200 AC: 305AN: 152134Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000558 AC: 139AN: 248902Hom.: 1 AF XY: 0.000342 AC XY: 46AN XY: 134596
GnomAD4 exome AF: 0.000215 AC: 314AN: 1458116Hom.: 1 Cov.: 32 AF XY: 0.000168 AC XY: 122AN XY: 724764
GnomAD4 genome AF: 0.00200 AC: 305AN: 152252Hom.: 1 Cov.: 33 AF XY: 0.00187 AC XY: 139AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:2
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LINS1: BP4 -
Inborn genetic diseases Uncertain:1
The p.G18R variant (also known as c.52G>A), located in coding exon 1 of the LINS gene, results from a G to A substitution at nucleotide position 52. The glycine at codon 18 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
LINS1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at