rs116422150
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006059.4(LAMC3):c.1792G>A(p.Gly598Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00268 in 1,613,700 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
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.1792G>A | p.Gly598Arg | missense_variant | 10/28 | ENST00000361069.9 | |
LAMC3 | XM_011518121.2 | c.1792G>A | p.Gly598Arg | missense_variant | 10/28 | ||
LAMC3 | XM_006716921.3 | c.1792G>A | p.Gly598Arg | missense_variant | 10/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMC3 | ENST00000361069.9 | c.1792G>A | p.Gly598Arg | missense_variant | 10/28 | 2 | NM_006059.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00978 AC: 1488AN: 152130Hom.: 17 Cov.: 33
GnomAD3 exomes AF: 0.00337 AC: 841AN: 249576Hom.: 9 AF XY: 0.00287 AC XY: 388AN XY: 135268
GnomAD4 exome AF: 0.00194 AC: 2832AN: 1461452Hom.: 19 Cov.: 35 AF XY: 0.00182 AC XY: 1323AN XY: 727016
GnomAD4 genome ? AF: 0.00977 AC: 1487AN: 152248Hom.: 17 Cov.: 33 AF XY: 0.00935 AC XY: 696AN XY: 74440
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 05, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 24, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 27, 2017 | - - |
LAMC3-related condition Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 14, 2019 | This variant is classified as 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