chr3-14130839-G-A
Variant summary
Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_024334.3(TMEM43):c.180G>A(p.Thr60Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,613,730 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T60T) has been classified as Likely benign.
Frequency
Consequence
NM_024334.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- arrhythmogenic right ventricular dysplasia 5Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen, G2P
- autosomal dominant Emery-Dreifuss muscular dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- auditory neuropathy, autosomal dominant 3Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- Emery-Dreifuss muscular dystrophy 7, autosomal dominantInheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM43 | NM_024334.3 | c.180G>A | p.Thr60Thr | synonymous_variant | Exon 3 of 12 | ENST00000306077.5 | NP_077310.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM43 | ENST00000306077.5 | c.180G>A | p.Thr60Thr | synonymous_variant | Exon 3 of 12 | 1 | NM_024334.3 | ENSP00000303992.5 | ||
TMEM43 | ENST00000432444.2 | n.*210G>A | non_coding_transcript_exon_variant | Exon 4 of 13 | 3 | ENSP00000395617.1 | ||||
TMEM43 | ENST00000432444.2 | n.*210G>A | 3_prime_UTR_variant | Exon 4 of 13 | 3 | ENSP00000395617.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000358 AC: 9AN: 251094 AF XY: 0.0000590 show subpopulations
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461544Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 727014 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Arrhythmogenic right ventricular dysplasia 5 Benign:2
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Cardiomyopathy Benign:1
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not provided Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely 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