Variant rs3805476 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000523005.1(ENSG00000253736):n.69+5041G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,482 control chromosomes in the GnomAD database, including 2,659 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 0.18 ( 2652 hom., cov: 32)

Exomes 𝑓: 0.17 ( 7 hom. )

Consequence

ENSG00000253736
ENST00000523005.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.510

Variant links:

Genes affected

ENSG00000253736 (HGNC:):

ENSG00000253736 links:

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]

DUSP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP1	NM_004417.4 link	c.*673C>T		downstream_gene_variant		ENST00000239223.4	NP_004408.1	P28562B4DU40

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253736	ENST00000523005.1 link	n.69+5041G>A		intron_variant		3
DUSP1	ENST00000239223.4 link	c.*673C>T		downstream_gene_variant		1	NM_004417.4	ENSP00000239223.3		P28562

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

26971

AN:

151932

Hom.:

2639

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.153

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.392

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.166

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.193

GnomAD4 exome

AF:

0.174

AC:

AN:

432

Hom.:

Cov.:

AF XY:

0.165

AC XY:

AN XY:

260

show subpopulations

Gnomad4 FIN exome

AF:

0.174

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.178

AC:

27013

AN:

152050

Hom.:

2652

Cov.:

AF XY:

0.181

AC XY:

13435

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.225

Gnomad4 ASJ

AF:

0.308

Gnomad4 EAS

AF:

0.392

Gnomad4 SAS

AF:

0.267

Gnomad4 FIN

AF:

0.166

Gnomad4 NFE

AF:

0.157

Gnomad4 OTH

AF:

0.198

Alfa

AF:

0.143

Hom.:

563

Bravo

AF:

0.179

Asia WGS

AF:

0.343

AC:

1191

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.1

DANN

Benign

0.76

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over