Genetic Variant DUSP22:p.Pro195Leu (chr6-348917-C-T) – ACMG Classification: Likely_benign (-3 pts)

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6

The NM_001286555.3(DUSP22):c.584C>T(p.Pro195Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00473 in 1,610,170 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 0.0039 ( 0 hom., cov: 65)

Exomes 𝑓: 0.0048 ( 1 hom. )

Consequence

DUSP22
NM_001286555.3 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 4.19

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 Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.0049518645).

BP6

Variant 6-348917-C-T is Benign according to our data. Variant chr6-348917-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3042277.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DUSP22	NM_001286555.3 link	c.584C>T	p.Pro195Leu	missense_variant	Exon 7 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.584C>T	p.Pro195Leu	missense_variant	Exon 7 of 7	2	NM_001286555.3	ENSP00000397459.2		Q9NRW4-2

Frequencies

GnomAD3 genomes

AF:

0.00393

AC:

598

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000965

Gnomad AMI

AF:

0.0122

Gnomad AMR

AF:

0.00674

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00122

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00599

Gnomad OTH

AF:

0.00908

GnomAD3 exomes

AF:

0.00356

AC:

866

AN:

242994

Hom.:

AF XY:

0.00342

AC XY:

451

AN XY:

131708

show subpopulations

Gnomad AFR exome

AF:

0.000703

Gnomad AMR exome

AF:

0.00486

Gnomad ASJ exome

AF:

0.00222

Gnomad EAS exome

AF:

0.0000568

Gnomad SAS exome

AF:

0.000726

Gnomad FIN exome

AF:

0.00112

Gnomad NFE exome

AF:

0.00557

Gnomad OTH exome

AF:

0.00318

GnomAD4 exome

AF:

0.00481

AC:

7012

AN:

1457874

Hom.:

Cov.:

115

AF XY:

0.00464

AC XY:

3365

AN XY:

725042

show subpopulations

Gnomad4 AFR exome

AF:

0.000987

Gnomad4 AMR exome

AF:

0.00525

Gnomad4 ASJ exome

AF:

0.00249

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.000767

Gnomad4 FIN exome

AF:

0.00145

Gnomad4 NFE exome

AF:

0.00568

Gnomad4 OTH exome

AF:

0.00367

GnomAD4 genome

AF:

0.00393

AC:

598

AN:

152296

Hom.:

Cov.:

AF XY:

0.00391

AC XY:

291

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.000962

Gnomad4 AMR

AF:

0.00673

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00122

Gnomad4 NFE

AF:

0.00599

Gnomad4 OTH

AF:

0.00899

Alfa

AF:

0.00516

Hom.:

ExAC

AF:

0.00354

AC:

429

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DUSP22-related disorder

Benign:1

Aug 19, 2020

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_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Uncertain

0.99

FATHMM_MKL

Benign

0.70

LIST_S2

Benign

0.64

.;.;T;T

MetaRNN

Benign

0.0050

T;T;T;T

Sift4G

Uncertain

0.013

D;D;D;D

Polyphen

0.032

.;.;B;.

Vest4

0.43

MVP

0.41

GERP RS

4.8

gMVP

0.44

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