Variant chr1-161752414-C-T 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.624C>T(p.Thr208=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0645 in 1,611,540 control chromosomes in the GnomAD database, including 7,077 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 0.14 ( 2700 hom., cov: 32)

Exomes 𝑓: 0.057 ( 4377 hom. )

Consequence

DUSP12
NM_007240.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0210

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:55826): (ATF6 divergent transcript)

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=-0.85).

BP7

Synonymous conserved (PhyloP=-0.021 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DUSP12	NM_007240.3 linkuse as main transcript	c.624C>T	p.Thr208=	synonymous_variant	4/6	ENST00000367943.5
DUSP12	XM_005244862.4 linkuse as main transcript	c.234C>T	p.Thr78=	synonymous_variant	4/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUSP12	ENST00000367943.5 linkuse as main transcript	c.624C>T	p.Thr208=	synonymous_variant	4/6	1	NM_007240.3	P1
ATF6-DT	ENST00000702792.1 linkuse as main transcript	n.373-2047G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20806

AN:

151942

Hom.:

2689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.338

Gnomad AMI

AF:

0.0363

Gnomad AMR

AF:

0.0702

Gnomad ASJ

AF:

0.0334

Gnomad EAS

AF:

0.216

Gnomad SAS

AF:

0.0297

Gnomad FIN

AF:

0.0619

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0508

Gnomad OTH

AF:

0.104

GnomAD3 exomes

AF:

0.0748

AC:

18777

AN:

251170

Hom.:

1653

AF XY:

0.0664

AC XY:

9013

AN XY:

135784

show subpopulations

Gnomad AFR exome

AF:

0.341

Gnomad AMR exome

AF:

0.0374

Gnomad ASJ exome

AF:

0.0365

Gnomad EAS exome

AF:

0.230

Gnomad SAS exome

AF:

0.0227

Gnomad FIN exome

AF:

0.0607

Gnomad NFE exome

AF:

0.0441

Gnomad OTH exome

AF:

0.0560

GnomAD4 exome

AF:

0.0569

AC:

83087

AN:

1459480

Hom.:

4377

Cov.:

AF XY:

0.0552

AC XY:

40058

AN XY:

726158

show subpopulations

Gnomad4 AFR exome

AF:

0.341

Gnomad4 AMR exome

AF:

0.0407

Gnomad4 ASJ exome

AF:

0.0356

Gnomad4 EAS exome

AF:

0.161

Gnomad4 SAS exome

AF:

0.0249

Gnomad4 FIN exome

AF:

0.0578

Gnomad4 NFE exome

AF:

0.0475

Gnomad4 OTH exome

AF:

0.0738

GnomAD4 genome

AF:

0.137

AC:

20845

AN:

152060

Hom.:

2700

Cov.:

AF XY:

0.134

AC XY:

9972

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.339

Gnomad4 AMR

AF:

0.0699

Gnomad4 ASJ

AF:

0.0334

Gnomad4 EAS

AF:

0.216

Gnomad4 SAS

AF:

0.0291

Gnomad4 FIN

AF:

0.0619

Gnomad4 NFE

AF:

0.0508

Gnomad4 OTH

AF:

0.103

Alfa

AF:

0.0759

Hom.:

887

Bravo

AF:

0.148

Asia WGS

AF:

0.125

AC:

436

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.0

DANN

Benign

0.28

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