1-209615311-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000228.3(LAMB3):āc.3479A>Gā(p.His1160Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000519 in 1,614,016 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000228.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMB3 | NM_000228.3 | c.3479A>G | p.His1160Arg | missense_variant | 23/23 | ENST00000356082.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMB3 | ENST00000356082.9 | c.3479A>G | p.His1160Arg | missense_variant | 23/23 | 1 | NM_000228.3 | P1 | |
LAMB3 | ENST00000367030.7 | c.3479A>G | p.His1160Arg | missense_variant | 23/23 | 1 | P1 | ||
LAMB3 | ENST00000391911.5 | c.3479A>G | p.His1160Arg | missense_variant | 22/22 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000348 AC: 53AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000442 AC: 111AN: 251242Hom.: 0 AF XY: 0.000405 AC XY: 55AN XY: 135794
GnomAD4 exome AF: 0.000537 AC: 785AN: 1461786Hom.: 1 Cov.: 30 AF XY: 0.000524 AC XY: 381AN XY: 727212
GnomAD4 genome AF: 0.000348 AC: 53AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74368
ClinVar
Submissions by phenotype
Junctional epidermolysis bullosa Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at