rs873460

chr6-123403337-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006073.4(TRDN):c.1052-9660C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,986 control chromosomes in the GnomAD database, including 10,162 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (10162 hom., cov: 32)
• Consequence: TRDN NM_006073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

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]

TRDN-AS1 (HGNC:40592): (TRDN antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRDN	NM_006073.4	c.1052-9660C>T		intron_variant		ENST00000334268.9
TRDN	NM_001251987.2	c.1055-9660C>T		intron_variant
TRDN	NM_001407315.1	c.995-9660C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRDN	ENST00000334268.9	c.1052-9660C>T		intron_variant		1	NM_006073.4	A2
TRDN-AS1	ENST00000587106.6	n.56-8378G>A		intron_variant, non_coding_transcript_variant		5
TRDN	ENST00000662930.1	c.1055-9660C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54032 AN: 151868 Hom.: 10150 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.402

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.356 AC: 54071 AN: 151986 Hom.: 10162 Cov.: 32 AF XY: 0.346 AC XY: 25692 AN XY: 74300

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.405

Alfa AF: 0.405 Hom.: 16620

Bravo AF: 0.369

Asia WGS AF: 0.201 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.51
Dann	Benign	0.21

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs873460; hg19: chr6-123724482;