NM_001003892.3:c.201-4985G>A

Variant names:

• chr10-75049002-C-T
• rs7919006
• NM_001003892.3:c.201-4985G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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]

ENSG00000285810 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001003892.3. 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
	DUSP29	NM_001003892.3	MANE Select	c.201-4985G>A		intron	N/A	NP_001003892.1	Q68J44
	DUSP29	NM_001384909.1		c.201-4985G>A		intron	N/A	NP_001371838.1	Q68J44

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DUSP29	ENST00000338487.6	TSL:1 MANE Select	c.201-4985G>A		intron	N/A	ENSP00000340609.5	Q68J44
	DUSP29	ENST00000944289.1		c.201-4985G>A		intron	N/A	ENSP00000614348.1
	ENSG00000285810	ENST00000649504.1		n.92-2377C>T		intron	N/A

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

African (AFR) AF: 0.444 AC: 18403 AN: 41446

American (AMR) AF: 0.172 AC: 2634 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0820 AC: 284 AN: 3462

East Asian (EAS) AF: 0.253 AC: 1307 AN: 5164

South Asian (SAS) AF: 0.161 AC: 777 AN: 4826

European-Finnish (FIN) AF: 0.0494 AC: 524 AN: 10600

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0485 AC: 3295 AN: 67990

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.0923 Hom.: 5391

Bravo AF: 0.204

Asia WGS AF: 0.233 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.71
PhyloP100		-0.47
Mutation Taster		=100/0	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: rs7919006; hg19: chr10-76808760;