rs55741126
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006059.4(LAMC3):c.2438G>A(p.Ser813Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,614,128 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S813R) has been classified 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMC3 | NM_006059.4 | c.2438G>A | p.Ser813Asn | missense_variant | 14/28 | ENST00000361069.9 | NP_006050.3 | |
LAMC3 | XM_011518121.2 | c.2438G>A | p.Ser813Asn | missense_variant | 14/28 | XP_011516423.1 | ||
LAMC3 | XM_006716921.3 | c.2438G>A | p.Ser813Asn | missense_variant | 14/23 | XP_006716984.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMC3 | ENST00000361069.9 | c.2438G>A | p.Ser813Asn | missense_variant | 14/28 | 2 | NM_006059.4 | ENSP00000354360.4 |
Frequencies
GnomAD3 genomes AF: 0.00539 AC: 821AN: 152180Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00146 AC: 367AN: 251164Hom.: 2 AF XY: 0.00102 AC XY: 139AN XY: 135840
GnomAD4 exome AF: 0.000561 AC: 820AN: 1461830Hom.: 7 Cov.: 32 AF XY: 0.000439 AC XY: 319AN XY: 727230
GnomAD4 genome AF: 0.00541 AC: 824AN: 152298Hom.: 9 Cov.: 32 AF XY: 0.00516 AC XY: 384AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 22, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 22, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 16, 2022 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at