Variant 1-11501107-G-A 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.115G>A(p.Gly39Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0907 in 1,613,808 control chromosomes in the GnomAD database, including 10,523 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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 0.15 ( 2957 hom., cov: 32)

Exomes 𝑓: 0.084 ( 7566 hom. )

Consequence

DISP3
NM_020780.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.89

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:

ENSG00000285833 (HGNC:):

ENSG00000285833 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=0.005902976).

BP6

Variant 1-11501107-G-A is Benign according to our data. Variant chr1-11501107-G-A is described in ClinVar as [Benign]. Clinvar id is 3060426.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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.115G>A	p.Gly39Arg	missense_variant	2/21	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.115G>A	p.Gly39Arg	missense_variant	2/21	1	NM_020780.2	ENSP00000294484.6		Q9P2K9-1
ENSG00000285833	ENST00000649975.1 linkuse as main transcript	n.747C>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23393

AN:

151996

Hom.:

2952

Cov.:

show subpopulations

Gnomad AFR

AF:

0.346

Gnomad AMI

AF:

0.0822

Gnomad AMR

AF:

0.0746

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.0448

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.128

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.0680

Gnomad OTH

AF:

0.124

GnomAD3 exomes

AF:

0.105

AC:

26245

AN:

249026

Hom.:

2273

AF XY:

0.108

AC XY:

14608

AN XY:

135148

show subpopulations

Gnomad AFR exome

AF:

0.355

Gnomad AMR exome

AF:

0.0451

Gnomad ASJ exome

AF:

0.119

Gnomad EAS exome

AF:

0.0385

Gnomad SAS exome

AF:

0.204

Gnomad FIN exome

AF:

0.123

Gnomad NFE exome

AF:

0.0702

Gnomad OTH exome

AF:

0.0815

GnomAD4 exome

AF:

0.0841

AC:

122880

AN:

1461694

Hom.:

7566

Cov.:

AF XY:

0.0872

AC XY:

63373

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.354

Gnomad4 AMR exome

AF:

0.0484

Gnomad4 ASJ exome

AF:

0.122

Gnomad4 EAS exome

AF:

0.0405

Gnomad4 SAS exome

AF:

0.199

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.0663

Gnomad4 OTH exome

AF:

0.0996

GnomAD4 genome

AF:

0.154

AC:

23423

AN:

152114

Hom.:

2957

Cov.:

AF XY:

0.155

AC XY:

11562

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.346

Gnomad4 AMR

AF:

0.0745

Gnomad4 ASJ

AF:

0.117

Gnomad4 EAS

AF:

0.0447

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.128

Gnomad4 NFE

AF:

0.0680

Gnomad4 OTH

AF:

0.122

Alfa

AF:

0.0824

Hom.:

1248

Bravo

AF:

0.153

TwinsUK

AF:

0.0707

AC:

262

ALSPAC

AF:

0.0752

AC:

290

ESP6500AA

AF:

0.337

AC:

1260

ESP6500EA

AF:

0.0664

AC:

543

ExAC

AF:

0.112

AC:

13513

Asia WGS

AF:

0.147

AC:

512

AN:

3478

EpiCase

AF:

0.0726

EpiControl

AF:

0.0679

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 30, 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

0.086

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.70

CADD

Benign

4.4

DANN

Benign

0.20

DEOGEN2

Benign

0.0091

Eigen

Benign

-0.59

Eigen_PC

Benign

-0.49

FATHMM_MKL

Benign

0.74

LIST_S2

Benign

0.67

MetaRNN

Benign

0.0059

MetaSVM

Benign

-0.95

PrimateAI

Benign

0.32

PROVEAN

Benign

-1.1

REVEL

Benign

0.059

Sift

Benign

0.57

Sift4G

Benign

0.078

Polyphen

0.0

Vest4

0.050

MutPred

0.15

Gain of solvent accessibility (P = 0.019);

MPC

0.44

ClinPred

0.0050

GERP RS

4.8

Varity_R

0.065

gMVP

0.16

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