1-183243185-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005562.3(LAMC2):c.3367C>T(p.Leu1123Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00725 in 1,582,926 control chromosomes in the GnomAD database, including 619 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005562.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMC2 | NM_005562.3 | c.3367C>T | p.Leu1123Leu | synonymous_variant | Exon 23 of 23 | ENST00000264144.5 | NP_005553.2 | |
LAMC2 | XM_047420358.1 | c.3328+2794C>T | intron_variant | Intron 22 of 23 | XP_047276314.1 | |||
LAMC2 | XM_047420361.1 | c.3328+2794C>T | intron_variant | Intron 22 of 22 | XP_047276317.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0413 AC: 5497AN: 133102Hom.: 321 Cov.: 31
GnomAD3 exomes AF: 0.00923 AC: 2317AN: 251056Hom.: 127 AF XY: 0.00672 AC XY: 912AN XY: 135712
GnomAD4 exome AF: 0.00412 AC: 5975AN: 1449708Hom.: 295 Cov.: 31 AF XY: 0.00362 AC XY: 2609AN XY: 720912
GnomAD4 genome AF: 0.0413 AC: 5508AN: 133218Hom.: 324 Cov.: 31 AF XY: 0.0400 AC XY: 2626AN XY: 65730
ClinVar
Submissions by phenotype
not provided Benign:3
- -
- -
- -
not specified Benign:1
- -
Junctional epidermolysis bullosa Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at