NM_007207.6:c.*1070C>T

Variant names:

• chr1-221701342-G-A
• rs908857
• ENST00000891854.1:c.*1070C>T

Variant summary

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

The NM_007207.6(DUSP10):​c.*1070C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,314 control chromosomes in the GnomAD database, including 29,757 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 0.61 (29687 hom., cov: 30)
  • Exomes 𝑓: 0.58 (70 hom.)
• Consequence: DUSP10 NM_007207.6 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 7 publications found

Genes affected

DUSP10 (HGNC:3065): (dual specificity phosphatase 10) Dual specificity protein phosphatases inactivate their target kinases by dephosphorylating both the phosphoserine/threonine and phosphotyrosine residues. They negatively regulate members of the MAP kinase superfamily, which is associated with cellular proliferation and differentiation. Different members of this family of dual specificity phosphatases show distinct substrate specificities for MAP kinases, different tissue distribution and subcellular localization, and different modes of expression induction by extracellular stimuli. This gene product binds to and inactivates p38 and SAPK/JNK. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007207.6. 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
	DUSP10	NM_007207.6	MANE Select	c.*1070C>T		downstream_gene	N/A	NP_009138.1	Q9Y6W6-1
	DUSP10	NR_111939.2		n.*82C>T		downstream_gene	N/A
	DUSP10	NR_111940.2		n.*82C>T		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP10	ENST00000891854.1		c.*1070C>T		3_prime_UTR	Exon 4 of 4	ENSP00000561913.1
	DUSP10	ENST00000366899.4	TSL:1 MANE Select	c.*1070C>T		downstream_gene	N/A	ENSP00000355866.3	Q9Y6W6-1
	DUSP10	ENST00000468085.5	TSL:1	n.*1480C>T		downstream_gene	N/A	ENSP00000483812.1	A0A0B4J2F5

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92177 AN: 151762 Hom.: 29643 Cov.: 30

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.573

GnomAD4 exome AF: 0.581 AC: 252 AN: 434 Hom.: 70 AF XY: 0.580 AC XY: 152 AN XY: 262

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.575 AC: 245 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.608 AC: 92279 AN: 151880 Hom.: 29687 Cov.: 30 AF XY: 0.604 AC XY: 44824 AN XY: 74210

African (AFR) AF: 0.836 AC: 34608 AN: 41406

American (AMR) AF: 0.530 AC: 8080 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1772 AN: 3470

East Asian (EAS) AF: 0.488 AC: 2524 AN: 5176

South Asian (SAS) AF: 0.427 AC: 2057 AN: 4818

European-Finnish (FIN) AF: 0.562 AC: 5910 AN: 10514

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35383 AN: 67942

Other (OTH) AF: 0.572 AC: 1201 AN: 2098

Alfa AF: 0.544 Hom.: 88997

Bravo AF: 0.620

Asia WGS AF: 0.479 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.18
PhyloP100		0.28
Mutation Taster		=97/3	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs908857; hg19: chr1-221874684;