rs35766971
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006073.4(TRDN):c.1016G>A(p.Ser339Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00205 in 1,591,380 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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. S339S) has been classified as Likely benign.
Frequency
Consequence
NM_006073.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRDN | NM_006073.4 | c.1016G>A | p.Ser339Asn | missense_variant | 12/41 | ENST00000334268.9 | |
TRDN | NM_001251987.2 | c.1019G>A | p.Ser340Asn | missense_variant | 12/21 | ||
TRDN | NM_001407315.1 | c.959G>A | p.Ser320Asn | missense_variant | 11/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRDN | ENST00000334268.9 | c.1016G>A | p.Ser339Asn | missense_variant | 12/41 | 1 | NM_006073.4 | A2 | |
TRDN-AS1 | ENST00000587106.6 | n.572-1505C>T | intron_variant, non_coding_transcript_variant | 5 | |||||
TRDN | ENST00000662930.1 | c.1019G>A | p.Ser340Asn | missense_variant | 12/21 |
Frequencies
GnomAD3 genomes AF: 0.0114 AC: 1734AN: 152068Hom.: 37 Cov.: 32
GnomAD3 exomes AF: 0.00271 AC: 594AN: 219566Hom.: 12 AF XY: 0.00201 AC XY: 239AN XY: 119004
GnomAD4 exome AF: 0.00107 AC: 1534AN: 1439194Hom.: 35 Cov.: 30 AF XY: 0.000887 AC XY: 634AN XY: 714934
GnomAD4 genome AF: 0.0114 AC: 1736AN: 152186Hom.: 37 Cov.: 32 AF XY: 0.0107 AC XY: 793AN XY: 74406
ClinVar
Submissions by phenotype
not specified Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jan 15, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2016 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 24, 2014 | Ser340Asn in exon 12 of TRDN: This variant is not expected to have clinical sign ificance because it has been identified in 3.3% (123/3682) of African American c hromosomes from a broad population by the NHLBI Exome Sequencing Project (http:/ /evs.gs.washington.edu/EVS; dbSNP rs35766971). - |
TRDN-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 29, 2019 | 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). - |
Catecholaminergic polymorphic ventricular tachycardia 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2015 | 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. - |
Catecholaminergic polymorphic ventricular tachycardia 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jun 19, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at