rs563283912
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2
The NM_032737.4(LMNB2):c.1231C>T(p.Arg411Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000458 in 1,593,364 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R411H) has been classified as Benign.
Frequency
Consequence
NM_032737.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMNB2 | NM_032737.4 | c.1231C>T | p.Arg411Cys | missense_variant | 8/12 | ENST00000325327.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327.4 | c.1231C>T | p.Arg411Cys | missense_variant | 8/12 | 1 | NM_032737.4 | P1 | |
LMNB2 | ENST00000490554.5 | n.422C>T | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000109 AC: 23AN: 210190Hom.: 0 AF XY: 0.000139 AC XY: 16AN XY: 115506
GnomAD4 exome AF: 0.0000472 AC: 68AN: 1440992Hom.: 2 Cov.: 36 AF XY: 0.0000713 AC XY: 51AN XY: 715548
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152372Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74512
ClinVar
Submissions by phenotype
Lipodystrophy, partial, acquired, susceptibility to;C4225289:Progressive myoclonic epilepsy type 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at