rs3764582
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032737.4(LMNB2):c.55G>A(p.Ala19Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0249 in 1,089,934 control chromosomes in the GnomAD database, including 354 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.020 ( 43 hom., cov: 30)
Exomes 𝑓: 0.026 ( 311 hom. )
Consequence
LMNB2
NM_032737.4 missense
NM_032737.4 missense
Scores
1
1
9
Clinical Significance
Conservation
PhyloP100: -0.0210
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0034243166).
BP6
?
Variant 19-2456879-C-T is Benign according to our data. Variant chr19-2456879-C-T is described in ClinVar as [Benign]. Clinvar id is 447703.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0778 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMNB2 | NM_032737.4 | c.55G>A | p.Ala19Thr | missense_variant | 1/12 | ENST00000325327.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327.4 | c.55G>A | p.Ala19Thr | missense_variant | 1/12 | 1 | NM_032737.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0199 AC: 2918AN: 146428Hom.: 43 Cov.: 30
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0295 AC: 70AN: 2374Hom.: 0 AF XY: 0.0319 AC XY: 39AN XY: 1222
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GnomAD4 exome AF: 0.0257 AC: 24257AN: 943400Hom.: 311 Cov.: 30 AF XY: 0.0256 AC XY: 11408AN XY: 446376
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GnomAD4 genome ? AF: 0.0199 AC: 2918AN: 146534Hom.: 43 Cov.: 30 AF XY: 0.0198 AC XY: 1413AN XY: 71326
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 11, 2017 | - - |
Lipodystrophy, partial, acquired, susceptibility to;C4225289:Progressive myoclonic epilepsy type 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
D;N
PrimateAI
Pathogenic
D
Sift4G
Benign
T
Vest4
MPC
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at