chr6-56618979-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001723.7(DST):c.5055T>C(p.Asn1685Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00558 in 1,614,172 control chromosomes in the GnomAD database, including 417 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 232 hom., cov: 32)

Exomes 𝑓: 0.0031 ( 185 hom. )

Consequence

DST
NM_001723.7 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.147

Publications

1 publications found

Variant links:

Genes affected

DST (HGNC:1090): (dystonin) This gene encodes a member of the plakin protein family of adhesion junction plaque proteins. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene, but the full-length nature of some variants has not been defined. It has been reported that some isoforms are expressed in neural and muscle tissue, anchoring neural intermediate filaments to the actin cytoskeleton, and some isoforms are expressed in epithelial tissue, anchoring keratin-containing intermediate filaments to hemidesmosomes. Consistent with the expression, mice defective for this gene show skin blistering and neurodegeneration. [provided by RefSeq, Mar 2010]

DST Gene-Disease associations (from GenCC):

hereditary sensory and autonomic neuropathy type 6
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Orphanet, Ambry Genetics, G2P, ClinGen, Labcorp Genetics (formerly Invitae)
epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency
Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: PanelApp Australia, Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet

DST links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 6-56618979-A-G is Benign according to our data. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56618979-A-G is described in CliVar as Benign/Likely_benign. Clinvar id is 357568.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.147 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0997 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DST	NM_001723.7 link	c.5055T>C	p.Asn1685Asn	synonymous_variant	Exon 23 of 24	ENST00000370765.11	NP_001714.1	Q03001-3
DST	NM_001374736.1 link	c.4930-4495T>C		intron_variant	Intron 36 of 103	ENST00000680361.1	NP_001361665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DST	ENST00000370765.11 link	c.5055T>C	p.Asn1685Asn	synonymous_variant	Exon 23 of 24	1	NM_001723.7	ENSP00000359801.6		Q03001-3
DST	ENST00000680361.1 link	c.4930-4495T>C		intron_variant	Intron 36 of 103		NM_001374736.1	ENSP00000505098.1		A0A7P0T890

Frequencies

GnomAD3 genomes

AF:

0.0297

AC:

4526

AN:

152180

Hom.:

232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0135

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000382

Gnomad OTH

AF:

0.0239

GnomAD2 exomes

AF:

0.00780

AC:

1959

AN:

251114

AF XY:

0.00570

show subpopulations

Gnomad AFR exome

AF:

0.105

Gnomad AMR exome

AF:

0.00549

Gnomad ASJ exome

AF:

0.000298

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000326

Gnomad OTH exome

AF:

0.00359

GnomAD4 exome

AF:

0.00306

AC:

4470

AN:

1461874

Hom.:

185

Cov.:

AF XY:

0.00257

AC XY:

1871

AN XY:

727234

show subpopulations

African (AFR)

AF:

0.103

AC:

3435

AN:

33478

American (AMR)

AF:

0.00631

AC:

282

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.000459

AC:

AN:

26134

East Asian (EAS)

AF:

0.00

AC:

AN:

39698

South Asian (SAS)

AF:

0.000267

AC:

AN:

86256

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53418

Middle Eastern (MID)

AF:

0.00555

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.000232

AC:

258

AN:

1112002

Other (OTH)

AF:

0.00709

AC:

428

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

269

538

808

1077

1346

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

108

216

324

432

540

<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:

0.0298

AC:

4532

AN:

152298

Hom.:

232

Cov.:

AF XY:

0.0286

AC XY:

2132

AN XY:

74488

show subpopulations

African (AFR)

AF:

0.102

AC:

4246

AN:

41530

American (AMR)

AF:

0.0135

AC:

206

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.000288

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5196

South Asian (SAS)

AF:

0.00

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000382

AC:

AN:

68032

Other (OTH)

AF:

0.0237

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

202

404

605

807

1009

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

176

220

<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:

0.0111

Hom.:

Bravo

AF:

0.0343

Asia WGS

AF:

0.00751

AC:

AN:

3478

EpiCase

AF:

0.000545

EpiControl

AF:

0.0000593

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

May 06, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hereditary sensory and autonomic neuropathy type 6;C3809470:Epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency

Benign:1

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hereditary sensory and autonomic neuropathy type 6

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.13

(source)

DANN

Benign

0.31

PhyloP100

-0.15

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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