Variant 1-11519447-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_020780.2(DISP3):c.1982G>C(p.Gly661Ala) variant causes a missense change. The variant allele was found at a frequency of 0.152 in 1,613,636 control chromosomes in the GnomAD database, including 21,434 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.14 ( 1871 hom., cov: 32)

Exomes 𝑓: 0.15 ( 19563 hom. )

Consequence

DISP3
NM_020780.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 4.46

Variant links:

Genes affected

DISP3 (HGNC:29251): (dispatched RND transporter family member 3) Involved in negative regulation of neuron differentiation; positive regulation of lipid metabolic process; and positive regulation of neural precursor cell proliferation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

DISP3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002960056).

BP6

Variant 1-11519447-G-C is Benign according to our data. Variant chr1-11519447-G-C is described in ClinVar as [Benign]. Clinvar id is 3059525.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DISP3	NM_020780.2 linkuse as main transcript	c.1982G>C	p.Gly661Ala	missense_variant	8/21	ENST00000294484.7	NP_065831.1	Q9P2K9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DISP3	ENST00000294484.7 linkuse as main transcript	c.1982G>C	p.Gly661Ala	missense_variant	8/21	1	NM_020780.2	ENSP00000294484.6		Q9P2K9-1

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21638

AN:

152120

Hom.:

1871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.464

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.146

GnomAD3 exomes

AF:

0.161

AC:

40130

AN:

249310

Hom.:

4388

AF XY:

0.163

AC XY:

22111

AN XY:

135302

show subpopulations

Gnomad AFR exome

AF:

0.114

Gnomad AMR exome

AF:

0.0945

Gnomad ASJ exome

AF:

0.162

Gnomad EAS exome

AF:

0.465

Gnomad SAS exome

AF:

0.199

Gnomad FIN exome

AF:

0.121

Gnomad NFE exome

AF:

0.138

Gnomad OTH exome

AF:

0.148

GnomAD4 exome

AF:

0.154

AC:

224326

AN:

1461398

Hom.:

19563

Cov.:

AF XY:

0.155

AC XY:

112956

AN XY:

727006

show subpopulations

Gnomad4 AFR exome

AF:

0.112

Gnomad4 AMR exome

AF:

0.0971

Gnomad4 ASJ exome

AF:

0.156

Gnomad4 EAS exome

AF:

0.444

Gnomad4 SAS exome

AF:

0.206

Gnomad4 FIN exome

AF:

0.124

Gnomad4 NFE exome

AF:

0.144

Gnomad4 OTH exome

AF:

0.159

GnomAD4 genome

AF:

0.142

AC:

21635

AN:

152238

Hom.:

1871

Cov.:

AF XY:

0.144

AC XY:

10732

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.116

Gnomad4 AMR

AF:

0.107

Gnomad4 ASJ

AF:

0.153

Gnomad4 EAS

AF:

0.464

Gnomad4 SAS

AF:

0.225

Gnomad4 FIN

AF:

0.119

Gnomad4 NFE

AF:

0.139

Gnomad4 OTH

AF:

0.148

Alfa

AF:

0.139

Hom.:

478

Bravo

AF:

0.141

TwinsUK

AF:

0.142

AC:

527

ALSPAC

AF:

0.146

AC:

563

ESP6500AA

AF:

0.105

AC:

424

ESP6500EA

AF:

0.144

AC:

1209

ExAC

AF:

0.162

AC:

19622

Asia WGS

AF:

0.316

AC:

1098

AN:

3478

EpiCase

AF:

0.140

EpiControl

AF:

0.139

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DISP3-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

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

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

0.91

DEOGEN2

Benign

0.0039

Eigen

Benign

-0.35

Eigen_PC

Benign

-0.28

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.58

MetaRNN

Benign

0.0030

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.41

PROVEAN

Benign

-0.39

REVEL

Uncertain

0.30

Sift

Benign

0.33

Sift4G

Benign

0.28

Polyphen

0.52

Vest4

0.12

MPC

0.62

ClinPred

0.013

GERP RS

3.7

Varity_R

0.046

gMVP

0.32

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