chr12-12493587-G-A

Variant names:

• chr12-12493587-G-A
• rs12819116
• NM_030640.3:c.532-6400C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030640.3(DUSP16):​c.532-6400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,952 control chromosomes in the GnomAD database, including 7,577 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 0.30 (7577 hom., cov: 31)
• Consequence: DUSP16 NM_030640.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030640.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP16	NM_030640.3	MANE Select	c.532-6400C>T		intron	N/A	NP_085143.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP16	ENST00000298573.9	TSL:1 MANE Select	c.532-6400C>T		intron	N/A	ENSP00000298573.5
	DUSP16	ENST00000228862.3	TSL:5	c.368-6400C>T		intron	N/A	ENSP00000228862.3
	DUSP16	ENST00000545864.1	TSL:4	n.265-6400C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45999 AN: 151834 Hom.: 7577 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.303 AC: 46022 AN: 151952 Hom.: 7577 Cov.: 31 AF XY: 0.306 AC XY: 22753 AN XY: 74248

African (AFR) AF: 0.212 AC: 8773 AN: 41434

American (AMR) AF: 0.331 AC: 5058 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3472

East Asian (EAS) AF: 0.128 AC: 662 AN: 5174

South Asian (SAS) AF: 0.248 AC: 1193 AN: 4808

European-Finnish (FIN) AF: 0.442 AC: 4658 AN: 10550

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23544 AN: 67920

Other (OTH) AF: 0.302 AC: 636 AN: 2106

Alfa AF: 0.330 Hom.: 8963

Bravo AF: 0.294

Asia WGS AF: 0.171 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.39
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12819116; hg19: chr12-12646521;