rs200293412
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_032737.4(LMNB2):c.1247G>T(p.Arg416Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000255 in 1,598,960 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032737.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327.4 | c.1247G>T | p.Arg416Leu | missense_variant | Exon 8 of 12 | 1 | NM_032737.4 | ENSP00000327054.3 | ||
LMNB2 | ENST00000490554.5 | n.438G>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 | |||||
LMNB2 | ENST00000532465.1 | n.-162G>T | upstream_gene_variant | 3 | ||||||
LMNB2 | ENST00000527409.1 | n.*234G>T | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00148 AC: 324AN: 218582Hom.: 5 AF XY: 0.000992 AC XY: 119AN XY: 119990
GnomAD4 exome AF: 0.000259 AC: 374AN: 1446630Hom.: 6 Cov.: 36 AF XY: 0.000209 AC XY: 150AN XY: 718730
GnomAD4 genome AF: 0.000223 AC: 34AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74492
ClinVar
Submissions by phenotype
Lipodystrophy, partial, acquired, susceptibility to;C4225289:Progressive myoclonic epilepsy type 9 Benign:1
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not provided Benign:1
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LMNB2-related disorder Benign:1
This variant is classified as 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