rs10762651

Positions:

• chr10-75062359-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001003892.3(DUSP29):​c.-34-3811C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,168 control chromosomes in the GnomAD database, including 2,324 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 0.14 (2324 hom., cov: 32)
• Consequence: DUSP29 NM_001003892.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

DUSP29 (HGNC:23481): (dual specificity phosphatase 29) Enables protein homodimerization activity and protein tyrosine/serine/threonine phosphatase activity. Involved in protein dephosphorylation. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP29	NM_001003892.3	c.-34-3811C>T		intron_variant		ENST00000338487.6	NP_001003892.1
DUSP29	NM_001384909.1	c.-34-3811C>T		intron_variant			NP_001371838.1
DUSP29	XM_017016176.2	c.-34-3811C>T		intron_variant			XP_016871665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DUSP29	ENST00000338487.6	c.-34-3811C>T		intron_variant		1	NM_001003892.3	ENSP00000340609	P1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21626 AN: 152048 Hom.: 2307 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0953

Gnomad EAS AF: 0.0647

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.0482

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0835

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.143 AC: 21688 AN: 152168 Hom.: 2324 Cov.: 32 AF XY: 0.141 AC XY: 10519 AN XY: 74404

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0844

Gnomad4 ASJ AF: 0.0953

Gnomad4 EAS AF: 0.0649

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.0482

Gnomad4 NFE AF: 0.0835

Gnomad4 OTH AF: 0.129

Alfa AF: 0.100 Hom.: 365

Bravo AF: 0.145

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10762651; hg19: chr10-76822117;