Variant 12-12477747-TGGGC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_030640.3(DUSP16):c.1080_1083delGCCC(p.Pro361fs) variant causes a frameshift change. The variant allele was found at a frequency of 0.0235 in 1,613,570 control chromosomes in the GnomAD database, including 2,919 homozygotes. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. VPSVP360VP) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.026 ( 281 hom., cov: 32)

Exomes 𝑓: 0.023 ( 2638 hom. )

Consequence

DUSP16
NM_030640.3 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.84

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 12-12477747-TGGGC-T is Benign according to our data. Variant chr12-12477747-TGGGC-T is described in ClinVar as [Benign]. Clinvar id is 771457.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP16	NM_030640.3 link	c.1080_1083delGCCC	p.Pro361fs	frameshift_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 link	c.1080_1083delGCCC	p.Pro361fs	frameshift_variant	7/7	1	NM_030640.3	ENSP00000298573.5		Q9BY84-1
DUSP16	ENST00000228862 link	c.484_487delGCCC		3_prime_UTR_variant	6/6	5		ENSP00000228862.3		Q9BY84-2

Frequencies

GnomAD3 genomes

AF:

0.0256

AC:

3901

AN:

152194

Hom.:

279

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00454

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0667

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.143

Gnomad FIN

AF:

0.0291

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00398

Gnomad OTH

AF:

0.0330

GnomAD3 exomes

AF:

0.0456

AC:

11302

AN:

247784

Hom.:

1105

AF XY:

0.0446

AC XY:

5984

AN XY:

134188

show subpopulations

Gnomad AFR exome

AF:

0.00255

Gnomad AMR exome

AF:

0.109

Gnomad ASJ exome

AF:

0.00956

Gnomad EAS exome

AF:

0.195

Gnomad SAS exome

AF:

0.100

Gnomad FIN exome

AF:

0.0211

Gnomad NFE exome

AF:

0.00411

Gnomad OTH exome

AF:

0.0290

GnomAD4 exome

AF:

0.0232

AC:

33954

AN:

1461258

Hom.:

2638

AF XY:

0.0255

AC XY:

18548

AN XY:

726872

show subpopulations

Gnomad4 AFR exome

AF:

0.00263

Gnomad4 AMR exome

AF:

0.134

Gnomad4 ASJ exome

AF:

0.0138

Gnomad4 EAS exome

AF:

0.245

Gnomad4 SAS exome

AF:

0.123

Gnomad4 FIN exome

AF:

0.0268

Gnomad4 NFE exome

AF:

0.00336

Gnomad4 OTH exome

AF:

0.0326

GnomAD4 genome

AF:

0.0257

AC:

3911

AN:

152312

Hom.:

281

Cov.:

AF XY:

0.0306

AC XY:

2278

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.00452

Gnomad4 AMR

AF:

0.0670

Gnomad4 ASJ

AF:

0.0179

Gnomad4 EAS

AF:

0.250

Gnomad4 SAS

AF:

0.142

Gnomad4 FIN

AF:

0.0291

Gnomad4 NFE

AF:

0.00398

Gnomad4 OTH

AF:

0.0355

Alfa

AF:

0.0103

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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