chr6-123548568-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1

The NM_006073.4(TRDN):c.277C>T(p.Arg93Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,554,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R93S) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00055 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000070 ( 0 hom. )

Consequence

TRDN
NM_006073.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:2

Conservation

PhyloP100: 1.89

Publications

5 publications found

Variant links:

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 Gene-Disease associations (from GenCC):

catecholaminergic polymorphic ventricular tachycardia
Inheritance: AD, AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
catecholaminergic polymorphic ventricular tachycardia 5
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp
familial long QT syndrome
Inheritance: AR Classification: STRONG Submitted by: G2P
long QT syndrome
Inheritance: AR Classification: STRONG Submitted by: ClinGen

TRDN links:

ENSG00000285691 (HGNC:):

ENSG00000285691 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.010916054).

BP6

Variant 6-123548568-G-A is Benign according to our data. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187. Variant chr6-123548568-G-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 415187.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.000552 (83/150464) while in subpopulation AFR AF = 0.00193 (79/40928). AF 95% confidence interval is 0.00159. There are 0 homozygotes in GnomAd4. There are 40 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRDN	NM_006073.4 link	c.277C>T	p.Arg93Cys	missense_variant	Exon 3 of 41	ENST00000334268.9	NP_006064.2	Q13061-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRDN	ENST00000334268.9 link	c.277C>T	p.Arg93Cys	missense_variant	Exon 3 of 41	1	NM_006073.4	ENSP00000333984.5		Q13061-1

Frequencies

GnomAD3 genomes

AF:

0.000552

AC:

AN:

150352

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00194

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000664

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000148

Gnomad OTH

AF:

0.000966

GnomAD2 exomes

AF:

0.000187

AC:

AN:

186764

AF XY:

0.000169

show subpopulations

Gnomad AFR exome

AF:

0.00244

Gnomad AMR exome

AF:

0.000119

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000123

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000705

AC:

AN:

1404404

Hom.:

Cov.:

AF XY:

0.0000619

AC XY:

AN XY:

695198

show subpopulations

African (AFR)

AF:

0.00176

AC:

AN:

31784

American (AMR)

AF:

0.0000800

AC:

AN:

37490

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24874

East Asian (EAS)

AF:

0.0000533

AC:

AN:

37490

South Asian (SAS)

AF:

0.0000782

AC:

AN:

76746

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50898

Middle Eastern (MID)

AF:

0.000177

AC:

AN:

5634

European-Non Finnish (NFE)

AF:

0.0000259

AC:

AN:

1081544

Other (OTH)

AF:

0.0000518

AC:

AN:

57944

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.457

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000552

AC:

AN:

150464

Hom.:

Cov.:

AF XY:

0.000546

AC XY:

AN XY:

73292

show subpopulations

African (AFR)

AF:

0.00193

AC:

AN:

40928

American (AMR)

AF:

0.0000663

AC:

AN:

15084

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3464

East Asian (EAS)

AF:

0.00

AC:

AN:

5100

South Asian (SAS)

AF:

0.00

AC:

AN:

4782

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10124

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0000148

AC:

AN:

67690

Other (OTH)

AF:

0.000957

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000182

Hom.:

Bravo

AF:

0.000502

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.000234

AC:

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:2

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Apr 28, 2025

GeneDx

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Catecholaminergic polymorphic ventricular tachycardia 1

Benign:1

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Cardiovascular phenotype

Benign:1

Feb 21, 2020

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.41

BayesDel_noAF

Benign

-0.36

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.17

T;.;.;.

Eigen

Benign

-0.039

Eigen_PC

Benign

0.043

FATHMM_MKL

Uncertain

0.79

LIST_S2

Benign

0.83

T;T;T;T

M_CAP

Benign

0.013

MetaRNN

Benign

0.011

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.0

N;N;.;N

PhyloP100

1.9

PrimateAI

Benign

0.40

PROVEAN

Benign

-1.9

N;.;N;N

REVEL

Benign

0.073

Sift

Uncertain

0.0030

D;.;D;D

Sift4G

Uncertain

0.018

D;D;D;D

Polyphen

0.94

P;.;.;.

Vest4

0.18

MVP

0.34

ClinPred

0.036

GERP RS

3.3

Varity_R

0.19

gMVP

0.082

Mutation Taster

=92/8

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over