5-172771284-GTT-GT

Variant names:

• chr5-172771284-GT-G
• rs28372789
• ENST00000523005.1:n.70-6207delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000523005.1(ENSG00000253736):​n.70-6207delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 200,342 control chromosomes in the GnomAD database, including 16,408 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.37 (11849 hom., cov: 0)
  • Exomes 𝑓: 0.40 (4559 hom.)
• 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523005.1. 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
	DUSP1	NM_004417.4	MANE Select	c.-333delA		upstream_gene	N/A	NP_004408.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253736	ENST00000523005.1	TSL:3	n.70-6207delT		intron	N/A
	DUSP1	ENST00000239223.4	TSL:1 MANE Select	c.-333delA		upstream_gene	N/A	ENSP00000239223.3

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56659 AN: 151232 Hom.: 11848 Cov.: 0

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.402

GnomAD4 exome AF: 0.397 AC: 19434 AN: 49000 Hom.: 4559 AF XY: 0.405 AC XY: 10080 AN XY: 24880

African (AFR) AF: 0.149 AC: 318 AN: 2130

American (AMR) AF: 0.357 AC: 473 AN: 1324

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 897 AN: 2186

East Asian (EAS) AF: 0.215 AC: 914 AN: 4242

South Asian (SAS) AF: 0.361 AC: 479 AN: 1326

European-Finnish (FIN) AF: 0.412 AC: 1056 AN: 2562

Middle Eastern (MID) AF: 0.430 AC: 122 AN: 284

European-Non Finnish (NFE) AF: 0.439 AC: 13799 AN: 31428

Other (OTH) AF: 0.391 AC: 1376 AN: 3518

GnomAD4 genome AF: 0.374 AC: 56668 AN: 151342 Hom.: 11849 Cov.: 0 AF XY: 0.373 AC XY: 27572 AN XY: 73928

African (AFR) AF: 0.181 AC: 7471 AN: 41274

American (AMR) AF: 0.392 AC: 5979 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1577 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1320 AN: 5074

South Asian (SAS) AF: 0.385 AC: 1848 AN: 4796

European-Finnish (FIN) AF: 0.467 AC: 4884 AN: 10458

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32266 AN: 67714

Other (OTH) AF: 0.396 AC: 834 AN: 2106

Alfa AF: 0.298 Hom.: 878

Bravo AF: 0.362

Asia WGS AF: 0.298 AC: 1036 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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;