chr19-2431811-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4BP6_Moderate
The NM_032737.4(LMNB2):c.1682G>T(p.Arg561Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R561C) has been classified as Benign.
Frequency
Consequence
NM_032737.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMNB2 | NM_032737.4 | c.1682G>T | p.Arg561Leu | missense_variant | 10/12 | ENST00000325327.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327.4 | c.1682G>T | p.Arg561Leu | missense_variant | 10/12 | 1 | NM_032737.4 | P1 | |
LMNB2 | ENST00000475819.1 | n.19G>T | non_coding_transcript_exon_variant | 1/2 | 5 | ||||
LMNB2 | ENST00000532465.1 | n.274G>T | non_coding_transcript_exon_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249828Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135456
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461496Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 16AN XY: 727084
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
Lipodystrophy, partial, acquired, susceptibility to;C4225289:Progressive myoclonic epilepsy type 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 09, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at