rs33942096
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_002292.4(LAMB2):c.1764C>T(p.Pro588Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0222 in 1,613,746 control chromosomes in the GnomAD database, including 463 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002292.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMB2 | ENST00000305544.9 | c.1764C>T | p.Pro588Pro | synonymous_variant | Exon 14 of 32 | 1 | NM_002292.4 | ENSP00000307156.4 | ||
LAMB2 | ENST00000418109.5 | c.1764C>T | p.Pro588Pro | synonymous_variant | Exon 15 of 33 | 1 | ENSP00000388325.1 | |||
LAMB2 | ENST00000483321.1 | n.194C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 | |||||
LAMB2 | ENST00000488638.1 | n.-47C>T | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0162 AC: 2470AN: 152156Hom.: 33 Cov.: 32
GnomAD3 exomes AF: 0.0165 AC: 4141AN: 251034Hom.: 47 AF XY: 0.0163 AC XY: 2217AN XY: 135698
GnomAD4 exome AF: 0.0228 AC: 33359AN: 1461472Hom.: 430 Cov.: 36 AF XY: 0.0222 AC XY: 16108AN XY: 726994
GnomAD4 genome AF: 0.0162 AC: 2470AN: 152274Hom.: 33 Cov.: 32 AF XY: 0.0153 AC XY: 1138AN XY: 74462
ClinVar
Submissions by phenotype
Pierson syndrome;C3280113:LAMB2-related infantile-onset nephrotic syndrome Benign:2
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not provided Benign:2
This variant is associated with the following publications: (PMID: 20556798) -
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not specified Benign:1
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Kidney disorder Benign:1
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LAMB2-related infantile-onset nephrotic syndrome 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. -
Pierson syndrome 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