12-12511269-G-C

Position:

• chr12-12511269-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030640.3(DUSP16):​c.367+8593C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,850 control chromosomes in the GnomAD database, including 22,912 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 0.55 (22912 hom., cov: 30)
• Consequence: DUSP16 NM_030640.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP16	NM_030640.3	c.367+8593C>G		intron_variant		ENST00000298573.9	NP_085143.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DUSP16	ENST00000298573.9	c.367+8593C>G		intron_variant		1	NM_030640.3	ENSP00000298573	P1
DUSP16	ENST00000228862.3	c.367+8593C>G		intron_variant		5		ENSP00000228862

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82694 AN: 151732 Hom.: 22888 Cov.: 30

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.546

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.545 AC: 82775 AN: 151850 Hom.: 22912 Cov.: 30 AF XY: 0.549 AC XY: 40771 AN XY: 74234

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.547

Alfa AF: 0.428 Hom.: 1194

Bravo AF: 0.536

Asia WGS AF: 0.592 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.092
DANN	Benign	0.38

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

Other links and lift over

dbSNP: rs7137455; hg19: chr12-12664203;