chr1-183186400-G-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_005562.3(LAMC2):c.48G>C(p.Leu16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000324 in 1,605,472 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L16L) has been classified as Likely benign.
Frequency
Consequence
NM_005562.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMC2 | NM_005562.3 | c.48G>C | p.Leu16= | synonymous_variant | 1/23 | ENST00000264144.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMC2 | ENST00000264144.5 | c.48G>C | p.Leu16= | synonymous_variant | 1/23 | 1 | NM_005562.3 | P1 | |
LAMC2 | ENST00000493293.5 | c.48G>C | p.Leu16= | synonymous_variant | 1/22 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152082Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000929 AC: 22AN: 236696Hom.: 1 AF XY: 0.000123 AC XY: 16AN XY: 130446
GnomAD4 exome AF: 0.0000344 AC: 50AN: 1453390Hom.: 2 Cov.: 33 AF XY: 0.0000525 AC XY: 38AN XY: 723438
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152082Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74278
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at