19-2434925-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_032737.4(LMNB2):c.856-12G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000325 in 1,598,946 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 (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000035 ( 2 hom. )
Consequence
LMNB2
NM_032737.4 intron
NM_032737.4 intron
Scores
2
Splicing: ADA: 0.00001684
2
Clinical Significance
Conservation
PhyloP100: -2.61
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BP6
Variant 19-2434925-C-T is Benign according to our data. Variant chr19-2434925-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2202643.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 2 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMNB2 | NM_032737.4 | c.856-12G>A | intron_variant | ENST00000325327.4 | NP_116126.3 | |||
MIR7108 | NR_106958.1 | n.76G>A | non_coding_transcript_exon_variant | 1/1 | ||||
MIR7108 | unassigned_transcript_3191 use as main transcript | n.9G>A | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327.4 | c.856-12G>A | intron_variant | 1 | NM_032737.4 | ENSP00000327054.3 | ||||
LMNB2 | ENST00000490554.5 | n.35G>A | non_coding_transcript_exon_variant | 1/4 | 2 | |||||
MIR7108 | ENST00000614319.1 | n.76G>A | non_coding_transcript_exon_variant | 1/1 | 6 | |||||
LMNB2 | ENST00000527409.1 | n.492-12G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000721 AC: 16AN: 221896Hom.: 1 AF XY: 0.0000732 AC XY: 9AN XY: 122876
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GnomAD4 exome AF: 0.0000353 AC: 51AN: 1446680Hom.: 2 Cov.: 34 AF XY: 0.0000417 AC XY: 30AN XY: 719408
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74442
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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 | Oct 19, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at