rs1051849

Variant names:

• chr17-37513222-T-C
• rs1051849
• NM_007026.4:c.*353T>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.*353T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 249,120 control chromosomes in the GnomAD database, including 1,604 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 (931 hom., cov: 31)
  • Exomes 𝑓: 0.11 (673 hom.)
• Consequence: DUSP14 NM_007026.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• Publications: 14 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUSP14	NM_007026.4	c.*353T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000617516.5	NP_008957.1
DUSP14	XM_005256977.4	c.*353T>C		3_prime_UTR_variant	Exon 3 of 3		XP_005257034.1
DUSP14	XM_011524234.2	c.*353T>C		3_prime_UTR_variant	Exon 3 of 3		XP_011522536.1
DUSP14	XM_047435217.1	c.*353T>C		3_prime_UTR_variant	Exon 3 of 3		XP_047291173.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUSP14	ENST00000617516.5	c.*353T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_007026.4	ENSP00000478595.1
DUSP14	ENST00000613659.1	c.*353T>C		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000484091.1
DUSP14	ENST00000614411.1	c.*353T>C		3_prime_UTR_variant	Exon 2 of 2	2		ENSP00000477653.1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15559 AN: 152090 Hom.: 929 Cov.: 31

Gnomad AFR AF: 0.0573

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.117

GnomAD4 exome AF: 0.108 AC: 10433 AN: 96912 Hom.: 673 Cov.: 0 AF XY: 0.110 AC XY: 5340 AN XY: 48666

African (AFR) AF: 0.0557 AC: 167 AN: 3000

American (AMR) AF: 0.0944 AC: 401 AN: 4250

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 249 AN: 3000

East Asian (EAS) AF: 0.204 AC: 1211 AN: 5950

South Asian (SAS) AF: 0.114 AC: 388 AN: 3416

European-Finnish (FIN) AF: 0.0900 AC: 1690 AN: 18782

Middle Eastern (MID) AF: 0.101 AC: 38 AN: 378

European-Non Finnish (NFE) AF: 0.108 AC: 5701 AN: 52766

Other (OTH) AF: 0.109 AC: 588 AN: 5370

GnomAD4 genome AF: 0.102 AC: 15559 AN: 152208 Hom.: 931 Cov.: 31 AF XY: 0.103 AC XY: 7638 AN XY: 74406

African (AFR) AF: 0.0571 AC: 2374 AN: 41548

American (AMR) AF: 0.104 AC: 1585 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1263 AN: 5166

South Asian (SAS) AF: 0.134 AC: 643 AN: 4810

European-Finnish (FIN) AF: 0.0904 AC: 959 AN: 10610

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8068 AN: 68008

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.112 Hom.: 1635

Bravo AF: 0.104

Asia WGS AF: 0.170 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.0
DANN	Benign	0.81
PhyloP100		-0.88
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: rs1051849; hg19: chr17-35873324;