Variant 6-348906-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BP7

The NM_001286555.3(DUSP22):c.573G>A(p.Pro191Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.48 ( 0 hom., cov: 63)

Exomes 𝑓: 0.48 ( 2 hom. )

Failed GnomAD Quality Control

Consequence

DUSP22
NM_001286555.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.672

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 6-348906-G-A is Benign according to our data. Variant chr6-348906-G-A is described in ClinVar as [Benign]. Clinvar id is 3059480.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.672 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DUSP22	NM_001286555.3 link	c.573G>A	p.Pro191Pro	synonymous_variant	7/7	ENST00000419235.7	NP_001273484.1	Q9NRW4-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DUSP22	ENST00000419235.7 link	c.573G>A	p.Pro191Pro	synonymous_variant	7/7	2	NM_001286555.3	ENSP00000397459.2		Q9NRW4-2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

72779

AN:

151040

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.492

Gnomad AMI

AF:

0.489

Gnomad AMR

AF:

0.481

Gnomad ASJ

AF:

0.461

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.490

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.479

Gnomad OTH

AF:

0.482

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.478

AC:

695332

AN:

1453604

Hom.:

Cov.:

129

AF XY:

0.478

AC XY:

345854

AN XY:

722904

show subpopulations

Gnomad4 AFR exome

AF:

0.493

Gnomad4 AMR exome

AF:

0.485

Gnomad4 ASJ exome

AF:

0.462

Gnomad4 EAS exome

AF:

0.472

Gnomad4 SAS exome

AF:

0.489

Gnomad4 FIN exome

AF:

0.474

Gnomad4 NFE exome

AF:

0.478

Gnomad4 OTH exome

AF:

0.477

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.482

AC:

72836

AN:

151154

Hom.:

Cov.:

AF XY:

0.482

AC XY:

35631

AN XY:

73892

show subpopulations

Gnomad4 AFR

AF:

0.492

Gnomad4 AMR

AF:

0.481

Gnomad4 ASJ

AF:

0.461

Gnomad4 EAS

AF:

0.471

Gnomad4 SAS

AF:

0.490

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.479

Gnomad4 OTH

AF:

0.481

Alfa

AF:

0.478

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DUSP22-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 03, 2021

This variant is classified as 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

-0.86

CADD

Benign

7.3

DANN

Benign

0.70

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