chr19-2432452-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_032737.4(LMNB2):c.1554G>A(p.Thr518=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,476 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T518T) has been classified as Benign.
Frequency
Consequence
NM_032737.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMNB2 | NM_032737.4 | c.1554G>A | p.Thr518= | synonymous_variant | 9/12 | ENST00000325327.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327.4 | c.1554G>A | p.Thr518= | synonymous_variant | 9/12 | 1 | NM_032737.4 | P1 | |
LMNB2 | ENST00000532465.1 | n.146G>A | non_coding_transcript_exon_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151850Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251148Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135786
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461626Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 727136
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151850Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74164
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 | Dec 07, 2022 | - - |
LMNB2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 16, 2019 | 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