rs7919006

Positions:

• chr10-75049002-C-T

Variant summary

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

The NM_001003892.3(DUSP29):​c.201-4985G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,086 control chromosomes in the GnomAD database, including 4,835 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 0.18 (4835 hom., cov: 33)
• Consequence: DUSP29 NM_001003892.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

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]

(HGNC:):

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 = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DUSP29	NM_001003892.3	c.201-4985G>A		intron_variant		ENST00000338487.6
DUSP29	NM_001384909.1	c.201-4985G>A		intron_variant
DUSP29	XM_017016176.2	c.201-4180G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DUSP29	ENST00000338487.6	c.201-4985G>A		intron_variant		1	NM_001003892.3	P1
	ENST00000649504.1	n.92-2377C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27547 AN: 151970 Hom.: 4804 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0820

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0494

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.182 AC: 27639 AN: 152086 Hom.: 4835 Cov.: 33 AF XY: 0.180 AC XY: 13419 AN XY: 74378

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.0820

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0494

Gnomad4 NFE AF: 0.0485

Gnomad4 OTH AF: 0.160

Alfa AF: 0.0737 Hom.: 1489

Bravo AF: 0.204

Asia WGS AF: 0.233 AC: 809 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	0.36
DANN	Benign	0.71

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

Publications

LitVar

Other links and lift over

dbSNP: rs7919006; hg19: chr10-76808760;