Variant 18-67511785-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_032160.3(DSEL):c.2824C>T(p.Pro942Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,614,122 control chromosomes in the GnomAD database, including 166 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0081 ( 9 hom., cov: 33)

Exomes 𝑓: 0.013 ( 157 hom. )

Consequence

DSEL
NM_032160.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.994

Variant links:

Genes affected

DSEL (HGNC:18144): (dermatan sulfate epimerase like) Predicted to enable chondroitin-glucuronate 5-epimerase activity. Predicted to be involved in chondroitin sulfate metabolic process and dermatan sulfate metabolic process. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]

DSEL links:

ENSG00000263424 (HGNC:):

ENSG00000263424 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0035323203).

BP6

Variant 18-67511785-G-A is Benign according to our data. Variant chr18-67511785-G-A is described in ClinVar as [Benign]. Clinvar id is 783071.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DSEL	NM_032160.3 linkuse as main transcript	c.2824C>T	p.Pro942Ser	missense_variant	2/2	ENST00000310045.9	NP_115536.2	Q8IZU8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DSEL	ENST00000310045.9 linkuse as main transcript	c.2824C>T	p.Pro942Ser	missense_variant	2/2	2	NM_032160.3	ENSP00000310565.8		Q8IZU8
ENSG00000263424	ENST00000583493.1 linkuse as main transcript	n.1044G>A		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes

AF:

0.00811

AC:

1233

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00241

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00721

Gnomad ASJ

AF:

0.00979

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00353

Gnomad FIN

AF:

0.00321

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0134

Gnomad OTH

AF:

0.0110

GnomAD3 exomes

AF:

0.00928

AC:

2325

AN:

250616

Hom.:

AF XY:

0.00948

AC XY:

1287

AN XY:

135796

show subpopulations

Gnomad AFR exome

AF:

0.00222

Gnomad AMR exome

AF:

0.00639

Gnomad ASJ exome

AF:

0.00973

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00408

Gnomad FIN exome

AF:

0.00328

Gnomad NFE exome

AF:

0.0150

Gnomad OTH exome

AF:

0.0128

GnomAD4 exome

AF:

0.0126

AC:

18403

AN:

1461880

Hom.:

157

Cov.:

AF XY:

0.0124

AC XY:

9014

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00230

Gnomad4 AMR exome

AF:

0.00653

Gnomad4 ASJ exome

AF:

0.00922

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00376

Gnomad4 FIN exome

AF:

0.00442

Gnomad4 NFE exome

AF:

0.0149

Gnomad4 OTH exome

AF:

0.0108

GnomAD4 genome

AF:

0.00811

AC:

1234

AN:

152242

Hom.:

Cov.:

AF XY:

0.00795

AC XY:

592

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.00241

Gnomad4 AMR

AF:

0.00720

Gnomad4 ASJ

AF:

0.00979

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00353

Gnomad4 FIN

AF:

0.00321

Gnomad4 NFE

AF:

0.0134

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.0126

Hom.:

Bravo

AF:

0.00854

TwinsUK

AF:

0.00998

AC:

ALSPAC

AF:

0.0125

AC:

ESP6500AA

AF:

0.00182

AC:

ESP6500EA

AF:

0.0149

AC:

128

ExAC

AF:

0.00962

AC:

1168

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.0151

EpiControl

AF:

0.0132

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.83

Eigen

Benign

-0.43

Eigen_PC

Benign

-0.27

FATHMM_MKL

Uncertain

0.88

MetaRNN

Benign

0.0035

MetaSVM

Benign

-0.84

PrimateAI

Benign

0.34

PROVEAN

Benign

-0.51

REVEL

Benign

0.079

Sift

Benign

0.22

Sift4G

Benign

0.74

Vest4

0.044

MVP

0.38

MPC

0.13

ClinPred

0.0043

GERP RS

3.1

gMVP

0.31

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over