rs150465100
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_002292.4(LAMB2):c.5061G>T(p.Thr1687=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000304 in 1,613,970 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T1687T) has been classified as Likely benign.
Frequency
Consequence
NM_002292.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMB2 | NM_002292.4 | c.5061G>T | p.Thr1687= | synonymous_variant | 30/32 | ENST00000305544.9 | |
LAMB2 | XM_005265127.5 | c.5061G>T | p.Thr1687= | synonymous_variant | 31/33 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMB2 | ENST00000305544.9 | c.5061G>T | p.Thr1687= | synonymous_variant | 30/32 | 1 | NM_002292.4 | P1 | |
LAMB2 | ENST00000418109.5 | c.5061G>T | p.Thr1687= | synonymous_variant | 31/33 | 1 | P1 | ||
LAMB2 | ENST00000467506.5 | n.171G>T | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
LAMB2 | ENST00000498377.1 | n.716G>T | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000673 AC: 169AN: 251208Hom.: 5 AF XY: 0.000928 AC XY: 126AN XY: 135846
GnomAD4 exome AF: 0.000321 AC: 469AN: 1461684Hom.: 9 Cov.: 33 AF XY: 0.000476 AC XY: 346AN XY: 727152
GnomAD4 genome ? AF: 0.000144 AC: 22AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74468
ClinVar
Submissions by phenotype
Pierson syndrome;C3280113:LAMB2-related infantile-onset nephrotic syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 11, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 17, 2022 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 26, 2019 | - - |
LAMB2-related infantile-onset nephrotic syndrome Benign:1
Likely benign, 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Pierson syndrome Benign:1
Likely benign, 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at