Variant rs1063178 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_007240.3(DUSP12):c.510C>T(p.Tyr170Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 1,609,770 control chromosomes in the GnomAD database, including 93,685 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 0.35 ( 9292 hom., cov: 32)

Exomes 𝑓: 0.34 ( 84393 hom. )

Consequence

DUSP12
NM_007240.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.575

Variant links:

Genes affected

DUSP12 (HGNC:3067): (dual specificity phosphatase 12) The protein encoded by this gene is a member of the dual specificity protein phosphatase subfamily. These phosphatases inactivate their target kinases by dephosphorylating both the phosphoserine/threonine and phosphotyrosine residues. They negatively regulate members of the mitogen-activated protein (MAP) kinase superfamily (MAPK/ERK, SAPK/JNK, p38), which is associated with cellular proliferation and differentiation. Different members of the family of dual specificity phosphatases show distinct substrate specificities for various MAP kinases, different tissue distribution and subcellular localization, and different modes of inducibility of their expression by extracellular stimuli. This gene product is the human ortholog of the Saccharomyces cerevisiae YVH1 protein tyrosine phosphatase. It is localized predominantly in the nucleus, and is novel in that it contains, and is regulated by a zinc finger domain. [provided by RefSeq, Jul 2008]

DUSP12 links:

ATF6-DT (HGNC:):

ATF6-DT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP7

Synonymous conserved (PhyloP=0.575 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP12	NM_007240.3 linkuse as main transcript	c.510C>T	p.Tyr170Tyr	synonymous_variant	3/6	ENST00000367943.5	NP_009171.1	Q9UNI6
DUSP12	XM_005244862.4 linkuse as main transcript	c.120C>T	p.Tyr40Tyr	synonymous_variant	3/6		XP_005244919.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DUSP12	ENST00000367943.5 linkuse as main transcript	c.510C>T	p.Tyr170Tyr	synonymous_variant	3/6	1	NM_007240.3	ENSP00000356920.4		Q9UNI6

Frequencies

GnomAD3 genomes

AF:

0.347

AC:

52696

AN:

151800

Hom.:

9287

Cov.:

show subpopulations

Gnomad AFR

AF:

0.385

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.359

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.332

Gnomad OTH

AF:

0.346

GnomAD3 exomes

AF:

0.335

AC:

84034

AN:

250490

Hom.:

14682

AF XY:

0.338

AC XY:

45739

AN XY:

135410

show subpopulations

Gnomad AFR exome

AF:

0.391

Gnomad AMR exome

AF:

0.242

Gnomad ASJ exome

AF:

0.328

Gnomad EAS exome

AF:

0.476

Gnomad SAS exome

AF:

0.341

Gnomad FIN exome

AF:

0.305

Gnomad NFE exome

AF:

0.338

Gnomad OTH exome

AF:

0.338

GnomAD4 exome

AF:

0.337

AC:

490801

AN:

1457852

Hom.:

84393

Cov.:

AF XY:

0.338

AC XY:

244874

AN XY:

725348

show subpopulations

Gnomad4 AFR exome

AF:

0.388

Gnomad4 AMR exome

AF:

0.248

Gnomad4 ASJ exome

AF:

0.324

Gnomad4 EAS exome

AF:

0.497

Gnomad4 SAS exome

AF:

0.344

Gnomad4 FIN exome

AF:

0.303

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.336

GnomAD4 genome

AF:

0.347

AC:

52724

AN:

151918

Hom.:

9292

Cov.:

AF XY:

0.347

AC XY:

25751

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.385

Gnomad4 AMR

AF:

0.294

Gnomad4 ASJ

AF:

0.326

Gnomad4 EAS

AF:

0.481

Gnomad4 SAS

AF:

0.359

Gnomad4 FIN

AF:

0.312

Gnomad4 NFE

AF:

0.332

Gnomad4 OTH

AF:

0.342

Alfa

AF:

0.336

Hom.:

19748

Bravo

AF:

0.346

Asia WGS

AF:

0.381

AC:

1323

AN:

3478

EpiCase

AF:

0.349

EpiControl

AF:

0.340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

7.3

DANN

Benign

0.46

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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