Variant 12-12477673-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_030640.3(DUSP16):c.1158C>T(p.Ser386Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00862 in 1,614,028 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0066 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0088 ( 73 hom. )

Consequence

DUSP16
NM_030640.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.643

Variant links:

Genes affected

DUSP16 (HGNC:17909): (dual specificity phosphatase 16) This gene encodes a mitogen-activated protein kinase phosphatase that 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. The encoded protein specifically regulates the c-Jun amino-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) pathways.[provided by RefSeq, May 2010]

DUSP16 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 12-12477673-G-A is Benign according to our data. Variant chr12-12477673-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2642737.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.643 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP16	NM_030640.3 linkuse as main transcript	c.1158C>T	p.Ser386Ser	synonymous_variant	7/7	ENST00000298573.9	NP_085143.1	Q9BY84-1A0A024RAR2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DUSP16	ENST00000298573.9 linkuse as main transcript	c.1158C>T	p.Ser386Ser	synonymous_variant	7/7	1	NM_030640.3	ENSP00000298573.5		Q9BY84-1
DUSP16	ENST00000228862.3 linkuse as main transcript	c.*562C>T		3_prime_UTR_variant	6/6	5		ENSP00000228862.3		Q9BY84-2

Frequencies

GnomAD3 genomes

AF:

0.00663

AC:

1010

AN:

152250

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00188

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00759

Gnomad ASJ

AF:

0.0311

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00894

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00867

Gnomad OTH

AF:

0.00718

GnomAD3 exomes

AF:

0.00731

AC:

1836

AN:

251262

Hom.:

AF XY:

0.00719

AC XY:

976

AN XY:

135806

show subpopulations

Gnomad AFR exome

AF:

0.00148

Gnomad AMR exome

AF:

0.00668

Gnomad ASJ exome

AF:

0.0310

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00173

Gnomad FIN exome

AF:

0.00743

Gnomad NFE exome

AF:

0.00870

Gnomad OTH exome

AF:

0.0108

GnomAD4 exome

AF:

0.00882

AC:

12897

AN:

1461660

Hom.:

Cov.:

AF XY:

0.00861

AC XY:

6264

AN XY:

727124

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00657

Gnomad4 ASJ exome

AF:

0.0316

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00204

Gnomad4 FIN exome

AF:

0.00701

Gnomad4 NFE exome

AF:

0.00947

Gnomad4 OTH exome

AF:

0.0106

GnomAD4 genome

AF:

0.00663

AC:

1010

AN:

152368

Hom.:

Cov.:

AF XY:

0.00652

AC XY:

486

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.00188

Gnomad4 AMR

AF:

0.00751

Gnomad4 ASJ

AF:

0.0311

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00894

Gnomad4 NFE

AF:

0.00867

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00962

Hom.:

Bravo

AF:

0.00645

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00916

EpiControl

AF:

0.0102

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

DUSP16: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

6.1

DANN

Benign

0.55

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over