rs4641

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate

The NM_170707.4(LMNA):​c.1698C>A​(p.His566Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000716 in 1,396,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H566D) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 7.2e-7 ( 0 hom. )

Consequence

LMNA
NM_170707.4 missense, splice_region

Scores

4
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.60
Variant links:
Genes affected
LMNA (HGNC:6636): (lamin A/C) The protein encoded by this gene is part of the nuclear lamina, 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. Alternative splicing results in multiple transcript variants. Mutations in this gene lead to several diseases: Emery-Dreifuss muscular dystrophy, familial partial lipodystrophy, limb girdle muscular dystrophy, dilated cardiomyopathy, Charcot-Marie-Tooth disease, and Hutchinson-Gilford progeria syndrome. [provided by RefSeq, May 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in the LMNA gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 178 curated pathogenic missense variants (we use a threshold of 10). The gene has 69 curated benign missense variants. Gene score misZ: 2.3673 (below the threshold of 3.09). Trascript score misZ: 3.0905 (above the threshold of 3.09). GenCC associations: The gene is linked to familial partial lipodystrophy, Dunnigan type, autosomal recessive Emery-Dreifuss muscular dystrophy, LMNA-related cardiocutaneous progeria syndrome, atrioventricular block, dilated cardiomyopathy 1A, Emery-Dreifuss muscular dystrophy 2, autosomal dominant, atypical Werner syndrome, restrictive dermopathy 1, autosomal semi-dominant severe lipodystrophic laminopathy, Emery-Dreifuss muscular dystrophy 3, autosomal recessive, dilated cardiomyopathy, Charcot-Marie-Tooth disease type 2B1, dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome, arrhythmogenic right ventricular cardiomyopathy, familial isolated dilated cardiomyopathy, mandibuloacral dysplasia with type A lipodystrophy, autosomal dominant Emery-Dreifuss muscular dystrophy, heart-hand syndrome, Slovenian type, congenital muscular dystrophy due to LMNA mutation, lethal restrictive dermopathy, Hutchinson-Gilford progeria syndrome.
BP4
Computational evidence support a benign effect (MetaRNN=0.15535209).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LMNANM_005572.4 linkc.1698C>A p.His566Gln missense_variant Exon 10 of 10 ENST00000677389.1 NP_005563.1 P02545-2
LMNANM_170707.4 linkc.1698C>A p.His566Gln missense_variant, splice_region_variant Exon 10 of 12 ENST00000368300.9 NP_733821.1 P02545-1A0A384MQX1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LMNAENST00000677389.1 linkc.1698C>A p.His566Gln missense_variant Exon 10 of 10 NM_005572.4 ENSP00000503633.1 P02545-2
LMNAENST00000368300.9 linkc.1698C>A p.His566Gln missense_variant, splice_region_variant Exon 10 of 12 1 NM_170707.4 ENSP00000357283.4 P02545-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
7.16e-7
AC:
1
AN:
1396962
Hom.:
0
Cov.:
34
AF XY:
0.00
AC XY:
0
AN XY:
689076
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.27e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
CardioboostCm
Benign
0.034
BayesDel_addAF
Uncertain
0.11
D
BayesDel_noAF
Uncertain
-0.080
CADD
Benign
12
DANN
Benign
0.91
DEOGEN2
Benign
0.37
.;.;T;.;.;.;.
Eigen
Benign
-0.84
Eigen_PC
Benign
-0.84
FATHMM_MKL
Benign
0.57
D
LIST_S2
Benign
0.42
T;T;T;T;T;T;T
M_CAP
Uncertain
0.13
D
MetaRNN
Benign
0.16
T;T;T;T;T;T;T
MetaSVM
Benign
-0.65
T
MutationAssessor
Benign
0.83
L;.;L;L;.;.;.
PrimateAI
Benign
0.48
T
PROVEAN
Benign
0.77
N;.;N;N;N;N;N
REVEL
Uncertain
0.50
Sift
Benign
0.12
T;.;T;T;T;T;T
Sift4G
Benign
0.097
T;T;T;T;T;T;T
Polyphen
0.95
P;.;D;.;.;B;.
Vest4
0.32
MutPred
0.15
Gain of loop (P = 0.1069);.;Gain of loop (P = 0.1069);Gain of loop (P = 0.1069);.;.;.;
MVP
0.93
MPC
0.39
ClinPred
0.29
T
GERP RS
-3.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.038
gMVP
0.29

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-156107534; API