rs4794755

Variant names:

• chr17-37506879-T-C
• rs4794755
• NM_007026.4:c.-180-3798T>C

Variant summary

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

The NM_007026.4(DUSP14):​c.-180-3798T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,172 control chromosomes in the GnomAD database, including 940 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 0.10 (940 hom., cov: 32)
• Consequence: DUSP14 NM_007026.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 8 publications found

Genes affected

DUSP14 (HGNC:17007): (dual specificity phosphatase 14) Dual-specificity phosphatases (DUSPs) constitute a large heterogeneous subgroup of the type I cysteine-based protein-tyrosine phosphatase superfamily. DUSPs are characterized by their ability to dephosphorylate both tyrosine and serine/threonine residues. They have been implicated as major modulators of critical signaling pathways. DUSP14 contains the consensus DUSP C-terminal catalytic domain but lacks the N-terminal CH2 domain found in the MKP (mitogen-activated protein kinase phosphatase) class of DUSPs (see MIM 600714) (summary by Patterson et al., 2009 [PubMed 19228121]).[supplied by OMIM, Dec 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007026.4. 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
	DUSP14	NM_007026.4	MANE Select	c.-180-3798T>C		intron	N/A	NP_008957.1	Q6FI36

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP14	ENST00000617516.5	TSL:1 MANE Select	c.-180-3798T>C		intron	N/A	ENSP00000478595.1	O95147
	DUSP14	ENST00000613659.1	TSL:2	c.-180-3798T>C		intron	N/A	ENSP00000484091.1	O95147
	DUSP14	ENST00000908259.1		c.-180-3798T>C		intron	N/A	ENSP00000578318.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15623 AN: 152054 Hom.: 936 Cov.: 32

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.103 AC: 15622 AN: 152172 Hom.: 940 Cov.: 32 AF XY: 0.103 AC XY: 7685 AN XY: 74396

African (AFR) AF: 0.0551 AC: 2289 AN: 41544

American (AMR) AF: 0.104 AC: 1590 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1256 AN: 5160

South Asian (SAS) AF: 0.135 AC: 650 AN: 4818

European-Finnish (FIN) AF: 0.0913 AC: 969 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8192 AN: 67974

Other (OTH) AF: 0.121 AC: 256 AN: 2112

Alfa AF: 0.116 Hom.: 1117

Bravo AF: 0.103

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		0.19
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: rs4794755; hg19: chr17-35866985;