rs908857

Variant names:

• chr1-221701342-G-A
• rs908857
• NM_007207.6:c.*1070C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-221701342-G-A
• chr1-221701342-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUSP10	NM_007207.6	c.*1070C>T		downstream_gene_variant		ENST00000366899.4	NP_009138.1
DUSP10	XM_047442948.1	c.*1070C>T		downstream_gene_variant			XP_047298904.1
DUSP10	NR_111939.2	n.*82C>T		downstream_gene_variant
DUSP10	NR_111940.2	n.*82C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUSP10	ENST00000366899.4	c.*1070C>T		downstream_gene_variant		1	NM_007207.6	ENSP00000355866.3
DUSP10	ENST00000468085.5	n.*1480C>T		downstream_gene_variant		1		ENSP00000483812.1

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

Gnomad4 FIN exome AF: 0.575

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.572

Alfa AF: 0.525 Hom.: 35282

Bravo AF: 0.620

Asia WGS AF: 0.479 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs908857; hg19: chr1-221874684;