Variant rs2279269 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032160.3(DSEL):c.2017C>T(p.Pro673Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 1,613,254 control chromosomes in the GnomAD database, including 204,267 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.46 ( 17084 hom., cov: 33)

Exomes 𝑓: 0.50 ( 187183 hom. )

Consequence

DSEL
NM_032160.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.61

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.1463484E-5).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSEL	NM_032160.3 linkuse as main transcript	c.2017C>T	p.Pro673Ser	missense_variant	2/2	ENST00000310045.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSEL	ENST00000310045.9 linkuse as main transcript	c.2017C>T	p.Pro673Ser	missense_variant	2/2	2	NM_032160.3	P1
	ENST00000583493.1 linkuse as main transcript	n.1851G>A		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70462

AN:

151832

Hom.:

17069

Cov.:

show subpopulations

Gnomad AFR

AF:

0.325

Gnomad AMI

AF:

0.422

Gnomad AMR

AF:

0.457

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.513

Gnomad SAS

AF:

0.397

Gnomad FIN

AF:

0.604

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.517

GnomAD3 exomes

AF:

0.497

AC:

124365

AN:

250402

Hom.:

31680

AF XY:

0.498

AC XY:

67418

AN XY:

135404

show subpopulations

Gnomad AFR exome

AF:

0.315

Gnomad AMR exome

AF:

0.471

Gnomad ASJ exome

AF:

0.531

Gnomad EAS exome

AF:

0.521

Gnomad SAS exome

AF:

0.402

Gnomad FIN exome

AF:

0.600

Gnomad NFE exome

AF:

0.528

Gnomad OTH exome

AF:

0.514

GnomAD4 exome

AF:

0.503

AC:

735322

AN:

1461304

Hom.:

187183

Cov.:

AF XY:

0.502

AC XY:

364686

AN XY:

726996

show subpopulations

Gnomad4 AFR exome

AF:

0.315

Gnomad4 AMR exome

AF:

0.464

Gnomad4 ASJ exome

AF:

0.531

Gnomad4 EAS exome

AF:

0.534

Gnomad4 SAS exome

AF:

0.404

Gnomad4 FIN exome

AF:

0.601

Gnomad4 NFE exome

AF:

0.511

Gnomad4 OTH exome

AF:

0.505

GnomAD4 genome

AF:

0.464

AC:

70493

AN:

151950

Hom.:

17084

Cov.:

AF XY:

0.467

AC XY:

34647

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.325

Gnomad4 AMR

AF:

0.456

Gnomad4 ASJ

AF:

0.520

Gnomad4 EAS

AF:

0.512

Gnomad4 SAS

AF:

0.397

Gnomad4 FIN

AF:

0.604

Gnomad4 NFE

AF:

0.525

Gnomad4 OTH

AF:

0.522

Alfa

AF:

0.515

Hom.:

47031

Bravo

AF:

0.450

TwinsUK

AF:

0.507

AC:

1881

ALSPAC

AF:

0.502

AC:

1934

ESP6500AA

AF:

0.324

AC:

1427

ESP6500EA

AF:

0.517

AC:

4444

ExAC

AF:

0.493

AC:

59888

Asia WGS

AF:

0.460

AC:

1599

AN:

3478

EpiCase

AF:

0.546

EpiControl

AF:

0.536

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

DANN

Benign

0.75

Eigen

Benign

-0.99

Eigen_PC

Benign

-0.72

FATHMM_MKL

Benign

0.23

MetaRNN

Benign

0.000081

MetaSVM

Benign

-0.93

MutationTaster

Benign

1.0

PrimateAI

Benign

0.39

PROVEAN

Benign

0.70

REVEL

Benign

0.079

Sift

Benign

1.0

Sift4G

Benign

0.81

Vest4

0.0060

MPC

0.13

ClinPred

0.0038

GERP RS

2.9

gMVP

0.23

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over