rs4795205

Variant names:

• chr17-37491226-C-T
• rs4795205
• NM_007026.4:c.-181+1268C>T

Variant summary

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

The NM_007026.4(DUSP14):​c.-181+1268C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0951 in 152,258 control chromosomes in the GnomAD database, including 909 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 0.095 (909 hom., cov: 32)
• Consequence: DUSP14 NM_007026.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 5 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=-0.77).
• 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 rank	MANE	Protein	UniProt
DUSP14	NM_007026.4	c.-181+1268C>T		intron_variant	Intron 1 of 2	ENST00000617516.5	NP_008957.1
DUSP14	XM_011524234.2	c.-181+2271C>T		intron_variant	Intron 1 of 2		XP_011522536.1
DUSP14	XM_047435217.1	c.-181+1592C>T		intron_variant	Intron 1 of 2		XP_047291173.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUSP14	ENST00000617516.5	c.-181+1268C>T		intron_variant	Intron 1 of 2	1	NM_007026.4	ENSP00000478595.1
DUSP14	ENST00000613659.1	c.-582C>T		upstream_gene_variant		2		ENSP00000484091.1

Frequencies

GnomAD3 genomes AF: 0.0952 AC: 14484 AN: 152140 Hom.: 905 Cov.: 32

Gnomad AFR AF: 0.0257

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.0951 AC: 14485 AN: 152258 Hom.: 909 Cov.: 32 AF XY: 0.0963 AC XY: 7170 AN XY: 74458

African (AFR) AF: 0.0256 AC: 1065 AN: 41562

American (AMR) AF: 0.102 AC: 1565 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0980 AC: 340 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1260 AN: 5180

South Asian (SAS) AF: 0.136 AC: 658 AN: 4824

European-Finnish (FIN) AF: 0.0914 AC: 969 AN: 10596

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8257 AN: 68014

Other (OTH) AF: 0.118 AC: 250 AN: 2114

Alfa AF: 0.0986 Hom.: 621

Bravo AF: 0.0950

Asia WGS AF: 0.171 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		0.056
PromoterAI		0.042	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs4795205; hg19: chr17-35851332;