Variant rs1129923 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001319658.2(DUSP23):c.391G>A(p.Gly131Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0892 in 1,613,962 control chromosomes in the GnomAD database, including 7,125 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.072 ( 528 hom., cov: 32)

Exomes 𝑓: 0.091 ( 6597 hom. )

Consequence

DUSP23
NM_001319658.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 9.51

Variant links:

Genes affected

DUSP23 (HGNC:21480): (dual specificity phosphatase 23) Enables protein tyrosine/serine/threonine phosphatase activity. Involved in dephosphorylation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

DUSP23 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0019216537).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
DUSP23	NM_001319658.2 linkuse as main transcript	c.391G>A	p.Gly131Ser	missense_variant	2/2	ENST00000368107.2
DUSP23	NM_001319659.2 linkuse as main transcript	c.391G>A	p.Gly131Ser	missense_variant	3/3
DUSP23	NM_017823.5 linkuse as main transcript	c.391G>A	p.Gly131Ser	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
DUSP23	ENST00000368107.2 linkuse as main transcript	c.391G>A	p.Gly131Ser	missense_variant	2/2	1	NM_001319658.2	P1
DUSP23	ENST00000368108.7 linkuse as main transcript	c.391G>A	p.Gly131Ser	missense_variant	3/3	1		P1
DUSP23	ENST00000368109.5 linkuse as main transcript	c.391G>A	p.Gly131Ser	missense_variant	3/3	2		P1

Frequencies

GnomAD3 genomes

AF:

0.0718

AC:

10910

AN:

151958

Hom.:

529

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0151

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.0625

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.00520

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0962

Gnomad OTH

AF:

0.0762

GnomAD3 exomes

AF:

0.0848

AC:

21319

AN:

251476

Hom.:

1149

AF XY:

0.0892

AC XY:

12125

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.0135

Gnomad AMR exome

AF:

0.0400

Gnomad ASJ exome

AF:

0.121

Gnomad EAS exome

AF:

0.00446

Gnomad SAS exome

AF:

0.125

Gnomad FIN exome

AF:

0.136

Gnomad NFE exome

AF:

0.0972

Gnomad OTH exome

AF:

0.0924

GnomAD4 exome

AF:

0.0910

AC:

133102

AN:

1461884

Hom.:

6597

Cov.:

AF XY:

0.0926

AC XY:

67341

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.0138

Gnomad4 AMR exome

AF:

0.0430

Gnomad4 ASJ exome

AF:

0.122

Gnomad4 EAS exome

AF:

0.00239

Gnomad4 SAS exome

AF:

0.123

Gnomad4 FIN exome

AF:

0.135

Gnomad4 NFE exome

AF:

0.0936

Gnomad4 OTH exome

AF:

0.0866

GnomAD4 genome

AF:

0.0717

AC:

10904

AN:

152078

Hom.:

528

Cov.:

AF XY:

0.0734

AC XY:

5459

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.0150

Gnomad4 AMR

AF:

0.0623

Gnomad4 ASJ

AF:

0.122

Gnomad4 EAS

AF:

0.00521

Gnomad4 SAS

AF:

0.129

Gnomad4 FIN

AF:

0.135

Gnomad4 NFE

AF:

0.0962

Gnomad4 OTH

AF:

0.0754

Alfa

AF:

0.0908

Hom.:

1691

Bravo

AF:

0.0619

TwinsUK

AF:

0.0949

AC:

352

ALSPAC

AF:

0.0848

AC:

327

ESP6500AA

AF:

0.0166

AC:

ESP6500EA

AF:

0.0921

AC:

792

ExAC

AF:

0.0850

AC:

10325

Asia WGS

AF:

0.0640

AC:

224

AN:

3478

EpiCase

AF:

0.100

EpiControl

AF:

0.0972

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.49

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.36

Cadd

Pathogenic

Dann

Uncertain

1.0

DEOGEN2

Uncertain

0.45

T;T;T

Eigen

Pathogenic

0.79

Eigen_PC

Pathogenic

0.73

FATHMM_MKL

Uncertain

0.96

MetaRNN

Benign

0.0019

T;T;T

MetaSVM

Benign

-0.90

MutationAssessor

Uncertain

2.7

M;M;M

MutationTaster

Benign

5.5e-9

P;P;P

PrimateAI

Uncertain

0.69

PROVEAN

Pathogenic

-4.6

D;D;D

REVEL

Benign

0.27

Sift

Uncertain

0.013

D;D;D

Sift4G

Uncertain

0.022

D;D;D

Polyphen

1.0

D;D;D

Vest4

0.47

MPC

1.1

ClinPred

0.020

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.88

gMVP

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over