2-96143592-T-C

Variant names:

• chr2-96143592-T-C
• rs1724120
• NM_004418.4:c.*231A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 27 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004418.4. 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
	DUSP2	NM_004418.4	MANE Select	c.*231A>G		3_prime_UTR	Exon 4 of 4	NP_004409.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP2	ENST00000288943.5	TSL:1 MANE Select	c.*231A>G		3_prime_UTR	Exon 4 of 4	ENSP00000288943.4
	DUSP2	ENST00000718436.1		c.*231A>G		3_prime_UTR	Exon 4 of 4	ENSP00000520821.1
	DUSP2	ENST00000488952.1	TSL:2	n.*137A>G		downstream_gene	N/A

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

African (AFR) AF: 0.410 AC: 4913 AN: 11974

American (AMR) AF: 0.616 AC: 10501 AN: 17058

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 5988 AN: 12990

East Asian (EAS) AF: 0.753 AC: 21690 AN: 28796

South Asian (SAS) AF: 0.524 AC: 22711 AN: 43350

European-Finnish (FIN) AF: 0.652 AC: 18017 AN: 27642

Middle Eastern (MID) AF: 0.512 AC: 943 AN: 1840

European-Non Finnish (NFE) AF: 0.559 AC: 143855 AN: 257344

Other (OTH) AF: 0.558 AC: 13619 AN: 24424

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

African (AFR) AF: 0.411 AC: 17013 AN: 41382

American (AMR) AF: 0.578 AC: 8821 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1601 AN: 3466

East Asian (EAS) AF: 0.797 AC: 4091 AN: 5136

South Asian (SAS) AF: 0.522 AC: 2515 AN: 4814

European-Finnish (FIN) AF: 0.652 AC: 6879 AN: 10558

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.559 AC: 38002 AN: 67962

Other (OTH) AF: 0.545 AC: 1147 AN: 2104

Alfa AF: 0.548 Hom.: 72030

Bravo AF: 0.526

Asia WGS AF: 0.584 AC: 2032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.0
DANN	Benign	0.39
PhyloP100		-0.34
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: rs1724120; hg19: chr2-96809331;