rs7702178

Variant names:

• chr5-172769994-T-C
• rs7702178
• NM_004417.4:c.513+167A>G

Variant summary

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

The NM_004417.4(DUSP1):​c.513+167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,302 control chromosomes in the GnomAD database, including 2,426 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 0.17 (2426 hom., cov: 34)
• Consequence: DUSP1 NM_004417.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 7 publications found

Genes affected

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]

ENSG00000253736 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004417.4. 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
	DUSP1	NM_004417.4	MANE Select	c.513+167A>G		intron	N/A	NP_004408.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP1	ENST00000239223.4	TSL:1 MANE Select	c.513+167A>G		intron	N/A	ENSP00000239223.3
	DUSP1	ENST00000868089.1		c.513+167A>G		intron	N/A	ENSP00000538148.1
	DUSP1	ENST00000868090.1		c.513+167A>G		intron	N/A	ENSP00000538149.1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25272 AN: 152184 Hom.: 2416 Cov.: 34

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.166 AC: 25294 AN: 152302 Hom.: 2426 Cov.: 34 AF XY: 0.170 AC XY: 12632 AN XY: 74482

African (AFR) AF: 0.107 AC: 4430 AN: 41570

American (AMR) AF: 0.221 AC: 3376 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1066 AN: 3468

East Asian (EAS) AF: 0.396 AC: 2051 AN: 5180

South Asian (SAS) AF: 0.270 AC: 1305 AN: 4832

European-Finnish (FIN) AF: 0.166 AC: 1762 AN: 10610

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10697 AN: 68012

Other (OTH) AF: 0.190 AC: 403 AN: 2116

Alfa AF: 0.163 Hom.: 2689

Bravo AF: 0.166

Asia WGS AF: 0.344 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.8
DANN	Benign	0.66
PhyloP100		-0.14
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs7702178; hg19: chr5-172196997; COSMIC: COSV107264142;