rs28372789

Variant names:

• chr5-172771284-GTT-G
• rs28372789
• ENST00000523005.1:n.70-6207_70-6206delTT

Your query was ambiguous. Multiple possible variants found:

• chr5-172771284-GTT-G
• chr5-172771284-GTT-GT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000523005.1(ENSG00000253736):​n.70-6207_70-6206delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000253736 ENST00000523005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855
• Publications: 2 publications found

Genes affected

ENSG00000253736 (HGNC:):

DUSP1 (HGNC:3064): (dual specificity phosphatase 1) The protein encoded by this gene is a phosphatase with dual specificity for tyrosine and threonine. The encoded protein can dephosphorylate MAP kinase MAPK1/ERK2, which results in its involvement in several cellular processes. This protein appears to play an important role in the human cellular response to environmental stress as well as in the negative regulation of cellular proliferation. Finally, the encoded protein can make some solid tumors resistant to both chemotherapy and radiotherapy, making it a target for cancer therapy. [provided by RefSeq, Aug 2017]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUSP1	NM_004417.4	c.-334_-333delAA		upstream_gene_variant		ENST00000239223.4	NP_004408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253736	ENST00000523005.1	n.70-6207_70-6206delTT		intron_variant	Intron 1 of 1	3
DUSP1	ENST00000239223.4	c.-334_-333delAA		upstream_gene_variant		1	NM_004417.4	ENSP00000239223.3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 49220 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 24984

African (AFR) AF: 0.00 AC: 0 AN: 2132

American (AMR) AF: 0.00 AC: 0 AN: 1330

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2204

East Asian (EAS) AF: 0.00 AC: 0 AN: 4254

South Asian (SAS) AF: 0.00 AC: 0 AN: 1328

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2574

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 286

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 31578

Other (OTH) AF: 0.00 AC: 0 AN: 3534

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 878

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.85

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs28372789; hg19: chr5-172198287;