Variant 1-186401149-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_017847.6(ODR4):c.1000+2105C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00569 in 1,595,472 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0045 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0058 ( 33 hom. )

Consequence

ODR4
NM_017847.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.924

Variant links:

Genes affected

ODR4 (HGNC:24299): (odr-4 GPCR localization factor homolog) Predicted to be involved in protein localization. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ODR4 links:

ODR4 (HGNC:):

ODR4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.011060685).

BP6

Variant 1-186401149-C-G is Benign according to our data. Variant chr1-186401149-C-G is described in ClinVar as [Benign]. Clinvar id is 715470.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 33 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODR4	NM_017847.6 linkuse as main transcript	c.1000+2105C>G		intron_variant		ENST00000287859.11	NP_060317.3	Q5SWX8-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
ODR4	ENST00000287859.11 linkuse as main transcript	c.1000+2105C>G	intron_variant	1	NM_017847.6	ENSP00000287859.6	Q5SWX8-1
ODR4	ENST00000367470.8 linkuse as main transcript	c.931+2105C>G	intron_variant	5		ENSP00000356440.3	Q5SWX8-2
ODR4	ENST00000419367.8 linkuse as main transcript	c.904+2105C>G	intron_variant	2		ENSP00000395084.3	Q5SWX8-4
ODR4	ENST00000478571.1 linkuse as main transcript	n.113+2105C>G	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.00449

AC:

683

AN:

152036

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000894

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00577

Gnomad ASJ

AF:

0.00634

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00763

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.00472

AC:

1174

AN:

248656

Hom.:

AF XY:

0.00493

AC XY:

665

AN XY:

134890

show subpopulations

Gnomad AFR exome

AF:

0.000840

Gnomad AMR exome

AF:

0.00494

Gnomad ASJ exome

AF:

0.00647

Gnomad EAS exome

AF:

0.0000557

Gnomad SAS exome

AF:

0.000788

Gnomad FIN exome

AF:

0.000465

Gnomad NFE exome

AF:

0.00759

Gnomad OTH exome

AF:

0.00579

GnomAD4 exome

AF:

0.00582

AC:

8402

AN:

1443318

Hom.:

Cov.:

AF XY:

0.00572

AC XY:

4104

AN XY:

717366

show subpopulations

Gnomad4 AFR exome

AF:

0.000936

Gnomad4 AMR exome

AF:

0.00501

Gnomad4 ASJ exome

AF:

0.00580

Gnomad4 EAS exome

AF:

0.0000255

Gnomad4 SAS exome

AF:

0.000756

Gnomad4 FIN exome

AF:

0.000783

Gnomad4 NFE exome

AF:

0.00687

Gnomad4 OTH exome

AF:

0.00521

GnomAD4 genome

AF:

0.00448

AC:

681

AN:

152154

Hom.:

Cov.:

AF XY:

0.00386

AC XY:

287

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.000891

Gnomad4 AMR

AF:

0.00569

Gnomad4 ASJ

AF:

0.00634

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.00763

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.00678

Hom.:

Bravo

AF:

0.00492

TwinsUK

AF:

0.00593

AC:

ALSPAC

AF:

0.00571

AC:

ESP6500AA

AF:

0.000834

AC:

ESP6500EA

AF:

0.00774

AC:

ExAC

AF:

0.00479

AC:

578

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.0108

EpiControl

AF:

0.00943

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 17, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.27

CADD

Benign

0.29

DANN

Benign

0.63

DEOGEN2

Benign

0.11

FATHMM_MKL

Benign

0.019

M_CAP

Benign

0.0026

MetaRNN

Benign

0.011

Sift4G

Pathogenic

0.0

Polyphen

0.99

Vest4

0.30

MVP

0.11

MPC

0.62

GERP RS

-1.4

Varity_R

0.050

gMVP

0.074

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