9-131049135-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006059.4(LAMC3):c.1630+5C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,526,112 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006059.4 splice_region, intron
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMC3 | NM_006059.4 | c.1630+5C>G | splice_region_variant, intron_variant | Intron 9 of 27 | ENST00000361069.9 | NP_006050.3 | ||
LAMC3 | XM_011518121.2 | c.1630+5C>G | splice_region_variant, intron_variant | Intron 9 of 27 | XP_011516423.1 | |||
LAMC3 | XM_006716921.3 | c.1630+5C>G | splice_region_variant, intron_variant | Intron 9 of 22 | XP_006716984.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00189 AC: 288AN: 152212Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00787 AC: 1230AN: 156228Hom.: 36 AF XY: 0.00612 AC XY: 504AN XY: 82314
GnomAD4 exome AF: 0.00126 AC: 1726AN: 1373782Hom.: 45 Cov.: 26 AF XY: 0.00110 AC XY: 748AN XY: 678992
GnomAD4 genome AF: 0.00190 AC: 290AN: 152330Hom.: 2 Cov.: 32 AF XY: 0.00183 AC XY: 136AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:2
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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
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LAMC3-related disorder Benign:1
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