NM_006073.4:c.1871-15G>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006073.4(TRDN):c.1871-15G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00321 in 1,264,438 control chromosomes in the GnomAD database, including 106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006073.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00822 AC: 1249AN: 151970Hom.: 24 Cov.: 32
GnomAD3 exomes AF: 0.00266 AC: 146AN: 54960Hom.: 1 AF XY: 0.00272 AC XY: 81AN XY: 29726
GnomAD4 exome AF: 0.00250 AC: 2786AN: 1112352Hom.: 79 Cov.: 20 AF XY: 0.00245 AC XY: 1323AN XY: 539638
GnomAD4 genome AF: 0.00834 AC: 1268AN: 152086Hom.: 27 Cov.: 32 AF XY: 0.00893 AC XY: 664AN XY: 74332
ClinVar
Submissions by phenotype
not specified Benign:5
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1871-15G>A in intron 35 of TRDN: This variant is not expected to have clinical s ignificance because it has been identified in 1.3% (42/3350) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http ://evs.gs.washington.edu/EVS; dbSNP rs59935057). -
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. -
Variant summary: TRDN c.1871-15G>A alters a non-conserved nucleotide located at a position not widely known to affect splicing. The variant allele was found at a frequency of 0.0027 in 54960 control chromosomes in the gnomAD database, including 1 homozygotes. The observed variant frequency is approximately 2 fold of the estimated maximal expected allele frequency for a pathogenic variant in TRDN causing Catecholaminergic Polymorphic Ventricular Tachycardia phenotype (0.0016), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.1871-15G>A in individuals affected with Catecholaminergic Polymorphic Ventricular Tachycardia and no experimental evidence demonstrating its impact on protein function have been reported. Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign. -
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Catecholaminergic polymorphic ventricular tachycardia 1 Benign:1
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Catecholaminergic polymorphic ventricular tachycardia 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at