chr5-172769994-T-C

Position:

• chr5-172769994-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP1	NM_004417.4	c.513+167A>G		intron_variant		ENST00000239223.4	NP_004408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DUSP1	ENST00000239223.4	c.513+167A>G		intron_variant		1	NM_004417.4	ENSP00000239223	P1
	ENST00000523005.1	n.69+6946T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.190

Alfa AF: 0.164 Hom.: 2155

Bravo AF: 0.166

Asia WGS AF: 0.344 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.8
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs7702178; hg19: chr5-172196997;