dbSNP rs908857: DUSP10:c.*1070C>T (chr1-221701342-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007207.6(DUSP10):c.*1070C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,314 control chromosomes in the GnomAD database, including 29,757 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 29687 hom., cov: 30)

Exomes 𝑓: 0.58 ( 70 hom. )

Consequence

DUSP10
NM_007207.6 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.281

Publications

7 publications found

Variant links:

Genes affected

DUSP10 (HGNC:3065): (dual specificity phosphatase 10) Dual specificity protein phosphatases inactivate their target kinases by dephosphorylating both the phosphoserine/threonine and phosphotyrosine residues. They negatively regulate members of the MAP kinase superfamily, which is associated with cellular proliferation and differentiation. Different members of this family of dual specificity phosphatases show distinct substrate specificities for MAP kinases, different tissue distribution and subcellular localization, and different modes of expression induction by extracellular stimuli. This gene product binds to and inactivates p38 and SAPK/JNK. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]

DUSP10 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
DUSP10	NM_007207.6 link	c.*1070C>T	downstream_gene_variant	ENST00000366899.4	NP_009138.1
DUSP10	NR_111939.2 link	n.*82C>T	downstream_gene_variant
DUSP10	NR_111940.2 link	n.*82C>T	downstream_gene_variant
DUSP10	XM_047442948.1 link	c.*1070C>T	downstream_gene_variant		XP_047298904.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUSP10	ENST00000366899.4 link	c.*1070C>T		downstream_gene_variant		1	NM_007207.6	ENSP00000355866.3
DUSP10	ENST00000468085.5 link	n.*1480C>T		downstream_gene_variant		1		ENSP00000483812.1

Frequencies

GnomAD3 genomes

AF:

0.607

AC:

92177

AN:

151762

Hom.:

29643

Cov.:

show subpopulations

Gnomad AFR

AF:

0.836

Gnomad AMI

AF:

0.652

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.511

Gnomad EAS

AF:

0.488

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.562

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.573

GnomAD4 exome

AF:

0.581

AC:

252

AN:

434

Hom.:

AF XY:

0.580

AC XY:

152

AN XY:

262

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.575

AC:

245

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.608

AC:

92279

AN:

151880

Hom.:

29687

Cov.:

AF XY:

0.604

AC XY:

44824

AN XY:

74210

show subpopulations

African (AFR)

AF:

0.836

AC:

34608

AN:

41406

American (AMR)

AF:

0.530

AC:

8080

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.511

AC:

1772

AN:

3470

East Asian (EAS)

AF:

0.488

AC:

2524

AN:

5176

South Asian (SAS)

AF:

0.427

AC:

2057

AN:

4818

European-Finnish (FIN)

AF:

0.562

AC:

5910

AN:

10514

Middle Eastern (MID)

AF:

0.514

AC:

151

AN:

294

European-Non Finnish (NFE)

AF:

0.521

AC:

35383

AN:

67942

Other (OTH)

AF:

0.572

AC:

1201

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1719

3439

5158

6878

8597

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

744

1488

2232

2976

3720

<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:

0.544

Hom.:

88997

Bravo

AF:

0.620

Asia WGS

AF:

0.479

AC:

1667

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

(source)

DANN

Benign

0.18

PhyloP100

0.28

Mutation Taster

=97/3

polymorphism

(source)

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over