rs998616364
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_032737.4(LMNB2):c.1332C>T(p.Pro444Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,610,654 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 (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000015 ( 0 hom. )
Consequence
LMNB2
NM_032737.4 synonymous
NM_032737.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.59
Genes affected
LMNB2 (HGNC:6638): (lamin B2) This gene encodes a B type nuclear lamin. The nuclear lamina consists of a two-dimensional matrix of proteins located next to the inner nuclear membrane. The lamin family of proteins make up the matrix and are highly conserved in evolution. During mitosis, the lamina matrix is reversibly disassembled as the lamin proteins are phosphorylated. Lamin proteins are thought to be involved in nuclear stability, chromatin structure and gene expression. Vertebrate lamins consist of two types, A and B. Mutations in this gene are associated with acquired partial lipodystrophy. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 19-2433976-G-A is Benign according to our data. Variant chr19-2433976-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 475772.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.59 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMNB2 | NM_032737.4 | c.1332C>T | p.Pro444Pro | synonymous_variant | 8/12 | ENST00000325327.4 | NP_116126.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327.4 | c.1332C>T | p.Pro444Pro | synonymous_variant | 8/12 | 1 | NM_032737.4 | ENSP00000327054.3 | ||
LMNB2 | ENST00000490554.5 | n.523C>T | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152256Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000414 AC: 1AN: 241510Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132088
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GnomAD4 exome AF: 0.0000151 AC: 22AN: 1458398Hom.: 0 Cov.: 36 AF XY: 0.0000138 AC XY: 10AN XY: 725606
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74388
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lipodystrophy, partial, acquired, susceptibility to;C4225289:Progressive myoclonic epilepsy type 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 22, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at