6-116436394-T-C

Variant names:

• chr6-116436394-T-C
• rs560644
• NM_013352.4:c.1926T>C

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_013352.4(DSE):​c.1926T>C​(p.Asn642Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 1,614,096 control chromosomes in the GnomAD database, including 710,142 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.96 (69521 hom., cov: 30)
  • Exomes 𝑓: 0.94 (640621 hom.)
• Consequence: DSE NM_013352.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0270

Genes affected

DSE (HGNC:21144): (dermatan sulfate epimerase) The protein encoded by this gene is a tumor-rejection antigen. It is localized to the endoplasmic reticulum and functions to convert D-glucuronic acid to L-iduronic acid during the biosynthesis of dermatan sulfate. This antigen possesses tumor epitopes capable of inducing HLA-A24-restricted and tumor-specific cytotoxic T lymphocytes in cancer patients and may be useful for specific immunotherapy. Mutations in this gene cause inmusculocontractural Ehlers-Danlos syndrome. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 9, and a paralogous gene exists on chromosome 18. [provided by RefSeq, Apr 2016]

ENSG00000285446 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 6-116436394-T-C is Benign according to our data. Variant chr6-116436394-T-C is described in ClinVar as [Benign]. Clinvar id is 1166942.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-116436394-T-C is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=-0.027 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSE	NM_013352.4	c.1926T>C	p.Asn642Asn	synonymous_variant	Exon 6 of 6	ENST00000644252.3	NP_037484.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSE	ENST00000644252.3	c.1926T>C	p.Asn642Asn	synonymous_variant	Exon 6 of 6		NM_013352.4	ENSP00000494147.2
ENSG00000285446	ENST00000644499.1	c.766+5201T>C		intron_variant	Intron 3 of 3			ENSP00000495266.1

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145283 AN: 152108 Hom.: 69461 Cov.: 30

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.953

GnomAD3 exomes AF: 0.954 AC: 239609 AN: 251204 Hom.: 114364 AF XY: 0.953 AC XY: 129442 AN XY: 135756

Gnomad AFR exome AF: 0.989

Gnomad AMR exome AF: 0.967

Gnomad ASJ exome AF: 0.967

Gnomad EAS exome AF: 0.999

Gnomad SAS exome AF: 0.978

Gnomad FIN exome AF: 0.959

Gnomad NFE exome AF: 0.929

Gnomad OTH exome AF: 0.947

GnomAD4 exome AF: 0.936 AC: 1368178 AN: 1461870 Hom.: 640621 Cov.: 94 AF XY: 0.937 AC XY: 681353 AN XY: 727240

Gnomad4 AFR exome AF: 0.990

Gnomad4 AMR exome AF: 0.966

Gnomad4 ASJ exome AF: 0.969

Gnomad4 EAS exome AF: 0.989

Gnomad4 SAS exome AF: 0.977

Gnomad4 FIN exome AF: 0.955

Gnomad4 NFE exome AF: 0.926

Gnomad4 OTH exome AF: 0.946

GnomAD4 genome AF: 0.955 AC: 145402 AN: 152226 Hom.: 69521 Cov.: 30 AF XY: 0.958 AC XY: 71277 AN XY: 74414

Gnomad4 AFR AF: 0.988

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.983

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.953

Alfa AF: 0.937 Hom.: 66324

Bravo AF: 0.956

Asia WGS AF: 0.989 AC: 3440 AN: 3478

EpiCase AF: 0.935

EpiControl AF: 0.932

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Ehlers-Danlos syndrome, musculocontractural type 2 Benign:2

Jul 30, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: 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	-0.64
CADD	Benign	1.0
DANN	Benign	0.56

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: rs560644; hg19: chr6-116757557;