5-172766871-A-G

Variant names:

• chr5-172766871-A-G
• rs178723
• ENST00000523005.1:n.69+3823A>G

Variant summary

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

The ENST00000523005.1(ENSG00000253736):​n.69+3823A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,170 control chromosomes in the GnomAD database, including 17,873 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 0.48 (17873 hom., cov: 33)
• Consequence: ENSG00000253736 ENST00000523005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 3 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 -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 = 0.536 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253736	ENST00000523005.1	TSL:3	n.69+3823A>G		intron	N/A
	ENSG00000253295	ENST00000733736.1		n.461+238A>G		intron	N/A
	DUSP1	ENST00000868089.1		c.*1187T>C		downstream_gene	N/A	ENSP00000538148.1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73106 AN: 152052 Hom.: 17859 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.481 AC: 73162 AN: 152170 Hom.: 17873 Cov.: 33 AF XY: 0.483 AC XY: 35902 AN XY: 74372

African (AFR) AF: 0.375 AC: 15569 AN: 41528

American (AMR) AF: 0.519 AC: 7932 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3468

East Asian (EAS) AF: 0.553 AC: 2861 AN: 5178

South Asian (SAS) AF: 0.520 AC: 2509 AN: 4822

European-Finnish (FIN) AF: 0.513 AC: 5430 AN: 10590

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.522 AC: 35470 AN: 67986

Other (OTH) AF: 0.507 AC: 1070 AN: 2110

Alfa AF: 0.503 Hom.: 11933

Bravo AF: 0.481

Asia WGS AF: 0.514 AC: 1788 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	2.4
DANN	Benign	0.74
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs178723; hg19: chr5-172193874;