2-96143592-T-C

Position:

• chr2-96143592-T-C

Variant summary

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

The NM_004418.4(DUSP2):​c.*231A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 577,316 control chromosomes in the GnomAD database, including 92,609 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 0.53 (22089 hom., cov: 32)
  • Exomes 𝑓: 0.57 (70520 hom.)
• Consequence: DUSP2 NM_004418.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

DUSP2 (HGNC:3068): (dual specificity phosphatase 2) 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 are 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 inactivates ERK1 and ERK2, is predominantly expressed in hematopoietic tissues, and is localized in the nucleus. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DUSP2	NM_004418.4	c.*231A>G		3_prime_UTR_variant	4/4	ENST00000288943.5
DUSP2	XM_017003546.2	c.*231A>G		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUSP2	ENST00000288943.5	c.*231A>G		3_prime_UTR_variant	4/4	1	NM_004418.4	P1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80705 AN: 151780 Hom.: 22049 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.544

GnomAD4 exome AF: 0.569 AC: 242237 AN: 425418 Hom.: 70520 Cov.: 4 AF XY: 0.566 AC XY: 126113 AN XY: 222656

Gnomad4 AFR exome AF: 0.410

Gnomad4 AMR exome AF: 0.616

Gnomad4 ASJ exome AF: 0.461

Gnomad4 EAS exome AF: 0.753

Gnomad4 SAS exome AF: 0.524

Gnomad4 FIN exome AF: 0.652

Gnomad4 NFE exome AF: 0.559

Gnomad4 OTH exome AF: 0.558

GnomAD4 genome AF: 0.532 AC: 80797 AN: 151898 Hom.: 22089 Cov.: 32 AF XY: 0.538 AC XY: 39946 AN XY: 74220

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.545

Alfa AF: 0.549 Hom.: 30536

Bravo AF: 0.526

Asia WGS AF: 0.584 AC: 2032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.0
DANN	Benign	0.39

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: rs1724120; hg19: chr2-96809331;