chr3-49125304-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_002292.4(LAMB2):c.2669C>T(p.Thr890Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0004 in 1,613,952 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_002292.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152236Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000764 AC: 192AN: 251278Hom.: 0 AF XY: 0.00104 AC XY: 141AN XY: 135866
GnomAD4 exome AF: 0.000418 AC: 611AN: 1461598Hom.: 6 Cov.: 35 AF XY: 0.000602 AC XY: 438AN XY: 727100
GnomAD4 genome AF: 0.000223 AC: 34AN: 152354Hom.: 1 Cov.: 33 AF XY: 0.000376 AC XY: 28AN XY: 74508
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
BS1 -
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Reported with a second variant (phase unknown) in a patient with minimal change disease and IgA nephropathy (Lata et al., 2018); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29204651) -
Pierson syndrome;C3280113:LAMB2-related infantile-onset nephrotic syndrome Benign:1
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LAMB2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at