rs1047981
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005562.3(LAMC2):c.2688G>A(p.Gln896Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 1,613,376 control chromosomes in the GnomAD database, including 46,122 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.2688G>A | p.Gln896Gln | synonymous_variant | Exon 18 of 23 | ENST00000264144.5 | NP_005553.2 | |
LAMC2 | NM_018891.3 | c.2688G>A | p.Gln896Gln | synonymous_variant | Exon 18 of 22 | NP_061486.2 | ||
LAMC2 | XM_047420358.1 | c.2688G>A | p.Gln896Gln | synonymous_variant | Exon 18 of 24 | XP_047276314.1 | ||
LAMC2 | XM_047420361.1 | c.2688G>A | p.Gln896Gln | synonymous_variant | Exon 18 of 23 | XP_047276317.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMC2 | ENST00000264144.5 | c.2688G>A | p.Gln896Gln | synonymous_variant | Exon 18 of 23 | 1 | NM_005562.3 | ENSP00000264144.4 | ||
LAMC2 | ENST00000493293.5 | c.2688G>A | p.Gln896Gln | synonymous_variant | Exon 18 of 22 | 1 | ENSP00000432063.1 |
Frequencies
GnomAD3 genomes AF: 0.292 AC: 44418AN: 152002Hom.: 8099 Cov.: 32
GnomAD3 exomes AF: 0.258 AC: 64719AN: 251246Hom.: 9965 AF XY: 0.248 AC XY: 33653AN XY: 135792
GnomAD4 exome AF: 0.213 AC: 311566AN: 1461256Hom.: 37989 Cov.: 33 AF XY: 0.214 AC XY: 155811AN XY: 726986
GnomAD4 genome AF: 0.293 AC: 44518AN: 152120Hom.: 8133 Cov.: 32 AF XY: 0.293 AC XY: 21783AN XY: 74358
ClinVar
Submissions by phenotype
not provided Benign:3
- -
- -
This variant is associated with the following publications: (PMID: 15370542, 11279058) -
not specified Benign:1
- -
Junctional epidermolysis bullosa, non-Herlitz type Benign:1
- -
Junctional epidermolysis bullosa gravis of Herlitz 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