chr9-131009252-T-TGGCACCGCG
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PM4BS1_Supporting
The NM_006059.4(LAMC3):c.42_50dup(p.Pro15_Ala17dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000299 in 1,293,078 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L13L) has been classified as Likely benign.
Frequency
Consequence
NM_006059.4 inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMC3 | NM_006059.4 | c.42_50dup | p.Pro15_Ala17dup | inframe_insertion | 1/28 | ENST00000361069.9 | |
LAMC3 | XM_006716921.3 | c.42_50dup | p.Pro15_Ala17dup | inframe_insertion | 1/23 | ||
LAMC3 | XM_011518121.2 | c.42_50dup | p.Pro15_Ala17dup | inframe_insertion | 1/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMC3 | ENST00000361069.9 | c.42_50dup | p.Pro15_Ala17dup | inframe_insertion | 1/28 | 2 | NM_006059.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00156 AC: 236AN: 151236Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000130 AC: 148AN: 1141734Hom.: 1 Cov.: 29 AF XY: 0.000118 AC XY: 65AN XY: 550962
GnomAD4 genome AF: 0.00157 AC: 238AN: 151344Hom.: 0 Cov.: 32 AF XY: 0.00157 AC XY: 116AN XY: 73934
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 13, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 30, 2022 | In-frame insertion of 3 amino acids in a non-repeat region; Has not been previously published as pathogenic or benign to our knowledge - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Occipital pachygyria and polymicrogyria Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Oct 11, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at