rs3088142

Variant names:

• chr10-75094806-C-T
• rs3088142
• NM_001363514.2:c.875G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-75094806-C-T
• chr10-75094806-C-G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001363514.2(DUSP13B):​c.875G>A​(p.Cys292Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 1,613,762 control chromosomes in the GnomAD database, including 179,702 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.53 (22654 hom., cov: 33)
  • Exomes 𝑓: 0.45 (157048 hom.)
• Consequence: DUSP13B NM_001363514.2 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.236
• Publications: 38 publications found

Genes affected

DUSP13B (HGNC:19681): (dual specificity phosphatase 13B) Members of the protein-tyrosine phosphatase superfamily cooperate with protein kinases to regulate cell proliferation and differentiation. This gene encodes a dual specificity phosphatase that acts on both phosphotyrosine and phosphoserine/threonine residues. The encoded protein is expressed in testis. [provided by RefSeq, Mar 2023]

DUSP13A (HGNC:56772): (dual specificity phosphatase 13A) Members of the protein-tyrosine phosphatase superfamily cooperate with protein kinases to regulate cell proliferation and differentiation. This gene encodes a dual specificity phosphatase that acts on both phosphotyrosine and phosphoserine/threonine residues. The encoded protein is expressed in skeletal muscle. [provided by RefSeq, Mar 2023]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=5.441111E-7).
• BP6: Variant 10-75094806-C-T is Benign according to our data. Variant chr10-75094806-C-T is described in ClinVar as Benign. ClinVar VariationId is 1179558.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363514.2. 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
	DUSP13B	NM_001363514.2	MANE Select	c.875G>A	p.Cys292Tyr	missense	Exon 4 of 4	NP_001350443.1	Q9UII6-5
	DUSP13B	NM_001007273.2		c.746G>A	p.Cys249Tyr	missense	Exon 6 of 6	NP_001007274.1	A0A9L9PXN7
	DUSP13B	NM_001320842.2		c.746G>A	p.Cys249Tyr	missense	Exon 7 of 7	NP_001307771.1	A0A9L9PXN7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP13B	ENST00000478873.7	TSL:5 MANE Select	c.875G>A	p.Cys292Tyr	missense	Exon 4 of 4	ENSP00000475626.1	Q9UII6-5
	DUSP13B	ENST00000473072.3	TSL:5	c.1124G>A	p.Cys375Tyr	missense	Exon 7 of 7	ENSP00000475732.2	U3KQB7
	DUSP13B	ENST00000472493.6	TSL:1	c.467G>A	p.Cys156Tyr	missense	Exon 4 of 4	ENSP00000444580.1	Q9UII6-1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80499 AN: 151970 Hom.: 22621 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.530

GnomAD2 exomes AF: 0.527 AC: 132191 AN: 250674 AF XY: 0.511

Gnomad AFR exome AF: 0.667

Gnomad AMR exome AF: 0.742

Gnomad ASJ exome AF: 0.449

Gnomad EAS exome AF: 0.907

Gnomad FIN exome AF: 0.467

Gnomad NFE exome AF: 0.414

Gnomad OTH exome AF: 0.507

GnomAD4 exome AF: 0.450 AC: 658482 AN: 1461674 Hom.: 157048 Cov.: 57 AF XY: 0.450 AC XY: 326964 AN XY: 727106

African (AFR) AF: 0.671 AC: 22473 AN: 33478

American (AMR) AF: 0.729 AC: 32592 AN: 44688

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 11879 AN: 26136

East Asian (EAS) AF: 0.912 AC: 36207 AN: 39696

South Asian (SAS) AF: 0.475 AC: 41000 AN: 86246

European-Finnish (FIN) AF: 0.461 AC: 24608 AN: 53384

Middle Eastern (MID) AF: 0.566 AC: 3262 AN: 5768

European-Non Finnish (NFE) AF: 0.412 AC: 457558 AN: 1111888

Other (OTH) AF: 0.479 AC: 28903 AN: 60390

GnomAD4 genome AF: 0.530 AC: 80580 AN: 152088 Hom.: 22654 Cov.: 33 AF XY: 0.534 AC XY: 39701 AN XY: 74362

African (AFR) AF: 0.664 AC: 27546 AN: 41468

American (AMR) AF: 0.621 AC: 9484 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1541 AN: 3470

East Asian (EAS) AF: 0.904 AC: 4675 AN: 5174

South Asian (SAS) AF: 0.487 AC: 2348 AN: 4820

European-Finnish (FIN) AF: 0.454 AC: 4804 AN: 10576

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28460 AN: 67990

Other (OTH) AF: 0.534 AC: 1126 AN: 2108

Alfa AF: 0.467 Hom.: 63632

Bravo AF: 0.555

TwinsUK AF: 0.410 AC: 1519

ALSPAC AF: 0.405 AC: 1559

ESP6500AA AF: 0.659 AC: 2903

ESP6500EA AF: 0.426 AC: 3663

ExAC AF: 0.518 AC: 62862

Asia WGS AF: 0.717 AC: 2493 AN: 3478

EpiCase AF: 0.429

EpiControl AF: 0.427

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Benign	-0.61	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	2.4
DANN	Benign	0.88
DEOGEN2	Benign	0.15	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.16	N
LIST_S2	Benign	0.32	T
MetaRNN	Benign	5.4e-7	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-1.4	N
PhyloP100		-0.24
PrimateAI	Benign	0.30	T
PROVEAN	Benign	1.3	N
REVEL	Benign	0.19
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0050	B
Vest4		0.056
MPC		0.25
ClinPred		0.00026	T
GERP RS		-2.2
Varity_R		0.11
gMVP		0.68
Mutation Taster		=97/3	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: rs3088142; hg19: chr10-76854564; COSMIC: COSV107346173; COSMIC: COSV107346173;