rs558713666
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_006073.4(TRDN):c.1056G>T(p.Pro352=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000411 in 1,604,256 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. P352P) has been classified as Likely benign.
Frequency
Consequence
NM_006073.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRDN | NM_006073.4 | c.1056G>T | p.Pro352= | synonymous_variant | 13/41 | ENST00000334268.9 | |
TRDN | NM_001251987.2 | c.1059G>T | p.Pro353= | synonymous_variant | 13/21 | ||
TRDN | NM_001407315.1 | c.999G>T | p.Pro333= | synonymous_variant | 12/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRDN | ENST00000334268.9 | c.1056G>T | p.Pro352= | synonymous_variant | 13/41 | 1 | NM_006073.4 | A2 | |
TRDN-AS1 | ENST00000587106.6 | n.55+4198C>A | intron_variant, non_coding_transcript_variant | 5 | |||||
TRDN | ENST00000662930.1 | c.1059G>T | p.Pro353= | synonymous_variant | 13/21 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 151730Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000424 AC: 10AN: 235646Hom.: 0 AF XY: 0.0000391 AC XY: 5AN XY: 127786
GnomAD4 exome AF: 0.0000275 AC: 40AN: 1452408Hom.: 0 Cov.: 30 AF XY: 0.0000305 AC XY: 22AN XY: 721814
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 151848Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 74216
ClinVar
Submissions by phenotype
Catecholaminergic polymorphic ventricular tachycardia 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2023 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2017 | 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