rs80356805
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001406993.1(LMNA):c.-121C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00138 in 1,613,524 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001406993.1 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMNA | NM_170707.4 | c.438C>T | p.Ala146Ala | synonymous_variant | Exon 2 of 12 | ENST00000368300.9 | NP_733821.1 | |
LMNA | NM_005572.4 | c.438C>T | p.Ala146Ala | synonymous_variant | Exon 2 of 10 | ENST00000677389.1 | NP_005563.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMNA | ENST00000368300.9 | c.438C>T | p.Ala146Ala | synonymous_variant | Exon 2 of 12 | 1 | NM_170707.4 | ENSP00000357283.4 | ||
LMNA | ENST00000677389.1 | c.438C>T | p.Ala146Ala | synonymous_variant | Exon 2 of 10 | NM_005572.4 | ENSP00000503633.1 |
Frequencies
GnomAD3 genomes AF: 0.00726 AC: 1105AN: 152180Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00176 AC: 441AN: 250598Hom.: 4 AF XY: 0.00135 AC XY: 183AN XY: 135562
GnomAD4 exome AF: 0.000763 AC: 1115AN: 1461224Hom.: 13 Cov.: 32 AF XY: 0.000663 AC XY: 482AN XY: 726878
GnomAD4 genome AF: 0.00729 AC: 1110AN: 152300Hom.: 10 Cov.: 32 AF XY: 0.00689 AC XY: 513AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:8
- -
- -
Ala146Ale in exon 2 of LMNA: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue, is not located within t he splice consensus sequence, and has been identified in 2.5% (108/4406) of Afri can American chromosomes from a broad population by the NHLBI Exome Sequencing P roject (http://evs.gs.washington.edu/EVS/; dbSNP rs80356805). -
- -
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
- -
- -
not provided Benign:4
- -
- -
- -
Variant summary: The LMNA c.438C>T (p.Ala146Ala) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 281/109760 control chromosomes (2 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0277371 (265/9554). This frequency is about 111 times the estimated maximal expected allele frequency of a pathogenic LMNA variant (0.00025), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as Benign. -
Cardiomyopathy Benign:2
- -
- -
Charcot-Marie-Tooth disease type 2 Benign:1
- -
LMNA-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Primary dilated cardiomyopathy Benign:1
- -
Cardiovascular phenotype Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at