10-75094806-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001363514.2(DUSP13B):c.875G>A(p.Cys292Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 1,613,762 control chromosomes in the GnomAD database, including 179,702 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.53 ( 22654 hom., cov: 33)

Exomes 𝑓: 0.45 ( 157048 hom. )

Consequence

DUSP13B
NM_001363514.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.236

Publications

38 publications found

Variant links:

Genes affected

DUSP13B (HGNC:19681): (dual specificity phosphatase 13B) Members of the protein-tyrosine phosphatase superfamily cooperate with protein kinases to regulate cell proliferation and differentiation. This gene encodes a dual specificity phosphatase that acts on both phosphotyrosine and phosphoserine/threonine residues. The encoded protein is expressed in testis. [provided by RefSeq, Mar 2023]

DUSP13B links:

DUSP13A (HGNC:56772): (dual specificity phosphatase 13A) Members of the protein-tyrosine phosphatase superfamily cooperate with protein kinases to regulate cell proliferation and differentiation. This gene encodes a dual specificity phosphatase that acts on both phosphotyrosine and phosphoserine/threonine residues. The encoded protein is expressed in skeletal muscle. [provided by RefSeq, Mar 2023]

DUSP13A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=5.441111E-7).

BP6

Variant 10-75094806-C-T is Benign according to our data. Variant chr10-75094806-C-T is described in ClinVar as Benign. ClinVar VariationId is 1179558.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUSP13B	NM_001363514.2 link	c.875G>A	p.Cys292Tyr	missense_variant	Exon 4 of 4	ENST00000478873.7	NP_001350443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUSP13B	ENST00000478873.7 link	c.875G>A	p.Cys292Tyr	missense_variant	Exon 4 of 4	5	NM_001363514.2	ENSP00000475626.1
DUSP13B	ENST00000473072.3 link	c.1124G>A	p.Cys375Tyr	missense_variant	Exon 7 of 7	5		ENSP00000475732.2

Frequencies

GnomAD3 genomes

AF:

0.530

AC:

80499

AN:

151970

Hom.:

22621

Cov.:

show subpopulations

Gnomad AFR

AF:

0.664

Gnomad AMI

AF:

0.465

Gnomad AMR

AF:

0.620

Gnomad ASJ

AF:

0.444

Gnomad EAS

AF:

0.904

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.454

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.530

GnomAD2 exomes

AF:

0.527

AC:

132191

AN:

250674

AF XY:

0.511

show subpopulations

Gnomad AFR exome

AF:

0.667

Gnomad AMR exome

AF:

0.742

Gnomad ASJ exome

AF:

0.449

Gnomad EAS exome

AF:

0.907

Gnomad FIN exome

AF:

0.467

Gnomad NFE exome

AF:

0.414

Gnomad OTH exome

AF:

0.507

GnomAD4 exome

AF:

0.450

AC:

658482

AN:

1461674

Hom.:

157048

Cov.:

AF XY:

0.450

AC XY:

326964

AN XY:

727106

show subpopulations

African (AFR)

AF:

0.671

AC:

22473

AN:

33478

American (AMR)

AF:

0.729

AC:

32592

AN:

44688

Ashkenazi Jewish (ASJ)

AF:

0.455

AC:

11879

AN:

26136

East Asian (EAS)

AF:

0.912

AC:

36207

AN:

39696

South Asian (SAS)

AF:

0.475

AC:

41000

AN:

86246

European-Finnish (FIN)

AF:

0.461

AC:

24608

AN:

53384

Middle Eastern (MID)

AF:

0.566

AC:

3262

AN:

5768

European-Non Finnish (NFE)

AF:

0.412

AC:

457558

AN:

1111888

Other (OTH)

AF:

0.479

AC:

28903

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

20162

40325

60487

80650

100812

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14406

28812

43218

57624

72030

<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:

0.530

AC:

80580

AN:

152088

Hom.:

22654

Cov.:

AF XY:

0.534

AC XY:

39701

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.664

AC:

27546

AN:

41468

American (AMR)

AF:

0.621

AC:

9484

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.444

AC:

1541

AN:

3470

East Asian (EAS)

AF:

0.904

AC:

4675

AN:

5174

South Asian (SAS)

AF:

0.487

AC:

2348

AN:

4820

European-Finnish (FIN)

AF:

0.454

AC:

4804

AN:

10576

Middle Eastern (MID)

AF:

0.585

AC:

172

AN:

294

European-Non Finnish (NFE)

AF:

0.419

AC:

28460

AN:

67990

Other (OTH)

AF:

0.534

AC:

1126

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1874

3747

5621

7494

9368

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

696

1392

2088

2784

3480

<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:

0.467

Hom.:

63632

Bravo

AF:

0.555

TwinsUK

AF:

0.410

AC:

1519

ALSPAC

AF:

0.405

AC:

1559

ESP6500AA

AF:

0.659

AC:

2903

ESP6500EA

AF:

0.426

AC:

3663

ExAC

AF:

0.518

AC:

62862

Asia WGS

AF:

0.717

AC:

2493

AN:

3478

EpiCase

AF:

0.429

EpiControl

AF:

0.427

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 17, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 21085059) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.51

CADD

Benign

2.4

(source)

DANN

Benign

0.88

DEOGEN2

Benign

0.15

T;T;T;.;T;T;.

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.16

LIST_S2

Benign

0.32

.;.;T;T;T;T;T

MetaRNN

Benign

5.4e-7

T;T;T;T;T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-1.4

N;N;.;.;.;N;.

PhyloP100

-0.24

PrimateAI

Benign

0.30

PROVEAN

Benign

1.3

N;.;N;.;.;.;N

REVEL

Benign

0.19

Sift

Benign

1.0

T;.;T;.;.;.;T

Sift4G

Benign

1.0

T;T;T;T;T;T;T

Polyphen

0.0050

B;B;.;.;.;B;B

Vest4

0.056

MPC

0.25

ClinPred

0.00026

GERP RS

-2.2

Varity_R

0.11

gMVP

0.68

Mutation Taster

=97/3

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