Genetic Variant DUSP22:p.Ser95Ser (chr6-348124-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS1

The NM_001286555.3(DUSP22):c.285C>T(p.Ser95Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0194 in 1,597,692 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.017 ( 0 hom., cov: 61)

Exomes 𝑓: 0.020 ( 1 hom. )

Consequence

DUSP22
NM_001286555.3 synonymous

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.05

Variant links:

Genes affected

DUSP22 (HGNC:16077): (dual specificity phosphatase 22) Enables non-membrane spanning protein tyrosine phosphatase activity and protein tyrosine kinase binding activity. Involved in several processes, including cellular response to epidermal growth factor stimulus; negative regulation of focal adhesion assembly; and negative regulation of non-membrane spanning protein tyrosine kinase activity. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Located in plasma membrane. Part of cytoplasm; filamentous actin; and leading edge of lamellipodium. [provided by Alliance of Genome Resources, Apr 2022]

DUSP22 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 6-348124-C-T is Benign according to our data. Variant chr6-348124-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3037645.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.05 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0166 (2516/151392) while in subpopulation NFE AF= 0.0224 (1514/67482). AF 95% confidence interval is 0.0215. There are 0 homozygotes in gnomad4. There are 1282 alleles in male gnomad4 subpopulation. Median coverage is 61. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUSP22	NM_001286555.3 link	c.285C>T	p.Ser95Ser	synonymous_variant	Exon 6 of 7	ENST00000419235.7	NP_001273484.1	Q9NRW4-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DUSP22	ENST00000419235.7 link	c.285C>T	p.Ser95Ser	synonymous_variant	Exon 6 of 7	2	NM_001286555.3	ENSP00000397459.2		Q9NRW4-2

Frequencies

GnomAD3 genomes

AF:

0.0166

AC:

2514

AN:

151274

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00379

Gnomad AMI

AF:

0.0188

Gnomad AMR

AF:

0.0146

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00393

Gnomad FIN

AF:

0.0476

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0224

Gnomad OTH

AF:

0.0211

GnomAD3 exomes

AF:

0.0164

AC:

4090

AN:

249176

Hom.:

AF XY:

0.0161

AC XY:

2169

AN XY:

134662

show subpopulations

Gnomad AFR exome

AF:

0.00283

Gnomad AMR exome

AF:

0.0106

Gnomad ASJ exome

AF:

0.0120

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.00268

Gnomad FIN exome

AF:

0.0448

Gnomad NFE exome

AF:

0.0214

Gnomad OTH exome

AF:

0.0199

GnomAD4 exome

AF:

0.0197

AC:

28422

AN:

1446300

Hom.:

Cov.:

AF XY:

0.0191

AC XY:

13732

AN XY:

719794

show subpopulations

Gnomad4 AFR exome

AF:

0.00308

Gnomad4 AMR exome

AF:

0.0110

Gnomad4 ASJ exome

AF:

0.0126

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.00317

Gnomad4 FIN exome

AF:

0.0447

Gnomad4 NFE exome

AF:

0.0217

Gnomad4 OTH exome

AF:

0.0157

GnomAD4 genome

AF:

0.0166

AC:

2516

AN:

151392

Hom.:

Cov.:

AF XY:

0.0173

AC XY:

1282

AN XY:

74014

show subpopulations

Gnomad4 AFR

AF:

0.00378

Gnomad4 AMR

AF:

0.0145

Gnomad4 ASJ

AF:

0.0133

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00414

Gnomad4 FIN

AF:

0.0476

Gnomad4 NFE

AF:

0.0224

Gnomad4 OTH

AF:

0.0209

Alfa

AF:

0.0147

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DUSP22-related disorder

Benign:1

Sep 25, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

3.7

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over