rs375961613
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_032737.4(LMNB2):c.428C>T(p.Thr143Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,609,798 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032737.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMNB2 | NM_032737.4 | c.428C>T | p.Thr143Met | missense_variant | 3/12 | ENST00000325327.4 | NP_116126.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327.4 | c.428C>T | p.Thr143Met | missense_variant | 3/12 | 1 | NM_032737.4 | ENSP00000327054.3 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000138 AC: 34AN: 246490Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 134070
GnomAD4 exome AF: 0.0000309 AC: 45AN: 1457514Hom.: 1 Cov.: 33 AF XY: 0.0000359 AC XY: 26AN XY: 724698
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74444
ClinVar
Submissions by phenotype
LMNB2-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 26, 2024 | The LMNB2 c.428C>T variant is predicted to result in the amino acid substitution p.Thr143Met. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.15% of alleles in individuals of East Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Lipodystrophy, partial, acquired, susceptibility to;C4225289:Progressive myoclonic epilepsy type 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at