chr6-123218586-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_006073.4(TRDN):c.*15C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000306 in 1,609,310 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 (★).
Frequency
Genomes: 𝑓 0.00036 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00030 ( 0 hom. )
Consequence
TRDN
NM_006073.4 3_prime_UTR
NM_006073.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.310
Genes affected
TRDN (HGNC:12261): (triadin) This gene encodes an integral membrane protein found in skeletal and cardiac muscle. The encoded protein plays a role in skeletal muscle excitation-contraction coupling as part of the calcium release complex and is required for normal skeletal muscle strength. This protein indirectly links triads and microtubules in skeletal muscle. Mutations in this gene are associated with cardiac arrythmia syndrome and some variants in this gene may be associated with sudden cardiac death. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 6-123218586-G-A is Benign according to our data. Variant chr6-123218586-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1212310.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.000301 (438/1457428) while in subpopulation MID AF= 0.00192 (11/5722). AF 95% confidence interval is 0.00108. There are 0 homozygotes in gnomad4_exome. There are 210 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRDN | NM_006073.4 | c.*15C>T | 3_prime_UTR_variant | 41/41 | ENST00000334268.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRDN | ENST00000334268.9 | c.*15C>T | 3_prime_UTR_variant | 41/41 | 1 | NM_006073.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000356 AC: 54AN: 151882Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000358 AC: 88AN: 245540Hom.: 0 AF XY: 0.000315 AC XY: 42AN XY: 133188
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GnomAD4 exome AF: 0.000301 AC: 438AN: 1457428Hom.: 0 Cov.: 31 AF XY: 0.000290 AC XY: 210AN XY: 725062
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GnomAD4 genome ? AF: 0.000356 AC: 54AN: 151882Hom.: 0 Cov.: 32 AF XY: 0.000310 AC XY: 23AN XY: 74160
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 03, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at