chr19-2435041-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_032737.4(LMNB2):c.815G>A(p.Arg272Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,610,378 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict 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. R272W) has been classified as Uncertain significance.
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 | UniProt |
---|---|---|---|---|---|---|---|
LMNB2 | NM_032737.4 | c.815G>A | p.Arg272Gln | missense_variant | 5/12 | ENST00000325327.4 | |
MIR7108 | NR_106958.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327.4 | c.815G>A | p.Arg272Gln | missense_variant | 5/12 | 1 | NM_032737.4 | P1 | |
LMNB2 | ENST00000527409.1 | n.451G>A | non_coding_transcript_exon_variant | 2/4 | 5 | ||||
LMNB2 | ENST00000534495.1 | n.453G>A | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
MIR7108 | ENST00000614319.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.000821 AC: 125AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000181 AC: 44AN: 243652Hom.: 0 AF XY: 0.000135 AC XY: 18AN XY: 132910
GnomAD4 exome AF: 0.0000871 AC: 127AN: 1458052Hom.: 1 Cov.: 40 AF XY: 0.0000827 AC XY: 60AN XY: 725496
GnomAD4 genome AF: 0.000821 AC: 125AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.000805 AC XY: 60AN XY: 74490
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 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at