chr9-131009306-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006059.4(LAMC3):c.92G>T(p.Arg31Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00373 in 1,443,812 control chromosomes in the GnomAD database, including 163 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_006059.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMC3 | NM_006059.4 | c.92G>T | p.Arg31Leu | missense_variant | 1/28 | ENST00000361069.9 | |
LAMC3 | XM_011518121.2 | c.92G>T | p.Arg31Leu | missense_variant | 1/28 | ||
LAMC3 | XM_006716921.3 | c.92G>T | p.Arg31Leu | missense_variant | 1/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMC3 | ENST00000361069.9 | c.92G>T | p.Arg31Leu | missense_variant | 1/28 | 2 | NM_006059.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0189 AC: 2867AN: 151734Hom.: 103 Cov.: 32
GnomAD3 exomes AF: 0.00147 AC: 90AN: 61058Hom.: 2 AF XY: 0.00131 AC XY: 47AN XY: 35756
GnomAD4 exome AF: 0.00194 AC: 2502AN: 1291970Hom.: 58 Cov.: 30 AF XY: 0.00168 AC XY: 1065AN XY: 635432
GnomAD4 genome AF: 0.0190 AC: 2887AN: 151842Hom.: 105 Cov.: 32 AF XY: 0.0183 AC XY: 1355AN XY: 74224
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 12, 2016 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at