rs4794755

chr17-37506879-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DUSP14	NM_007026.4	c.-180-3798T>C		intron_variant		ENST00000617516.5
DUSP14	XM_005256977.4	c.-180-3798T>C		intron_variant
DUSP14	XM_011524234.2	c.-180-3798T>C		intron_variant
DUSP14	XM_047435217.1	c.-180-3798T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUSP14	ENST00000617516.5	c.-180-3798T>C		intron_variant		1	NM_007026.4	P1
DUSP14	ENST00000613659.1	c.-180-3798T>C		intron_variant		2		P1

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

Gnomad4 AFR AF: 0.0551

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.121

Alfa AF: 0.115 Hom.: 609

Bravo AF: 0.103

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	11
Dann	Benign	0.80

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: rs4794755; hg19: chr17-35866985;