Variant chr19-48296961-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001364171.2(ODAD1):c.*15A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,569,652 control chromosomes in the GnomAD database, including 31,752 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 3872 hom., cov: 31)

Exomes 𝑓: 0.19 ( 27880 hom. )

Consequence

ODAD1
NM_001364171.2 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.87

Variant links:

Genes affected

ODAD1 (HGNC:26560): (outer dynein arm docking complex subunit 1) This gene encodes a coiled-coil domain-containing protein that is a component of the outer dynein arm docking complex in cilia cells. Mutations in this gene may cause primary ciliary dyskinesia 20. [provided by RefSeq, May 2013]

ODAD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 19-48296961-T-C is Benign according to our data. Variant chr19-48296961-T-C is described in ClinVar as [Benign]. Clinvar id is 262481.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODAD1	NM_001364171.2 linkuse as main transcript	c.*15A>G		3_prime_UTR_variant	16/16	ENST00000674294.1
ODAD1	NM_144577.4 linkuse as main transcript	c.*15A>G		3_prime_UTR_variant	14/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODAD1	ENST00000674294.1 linkuse as main transcript	c.*15A>G		3_prime_UTR_variant	16/16		NM_001364171.2	P2

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33195

AN:

151806

Hom.:

3868

Cov.:

show subpopulations

Gnomad AFR

AF:

0.289

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.190

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.191

GnomAD3 exomes

AF:

0.184

AC:

39530

AN:

215070

Hom.:

3949

AF XY:

0.187

AC XY:

21750

AN XY:

116294

show subpopulations

Gnomad AFR exome

AF:

0.285

Gnomad AMR exome

AF:

0.0863

Gnomad ASJ exome

AF:

0.189

Gnomad EAS exome

AF:

0.123

Gnomad SAS exome

AF:

0.182

Gnomad FIN exome

AF:

0.251

Gnomad NFE exome

AF:

0.199

Gnomad OTH exome

AF:

0.174

GnomAD4 exome

AF:

0.194

AC:

275149

AN:

1417728

Hom.:

27880

Cov.:

AF XY:

0.194

AC XY:

136349

AN XY:

701862

show subpopulations

Gnomad4 AFR exome

AF:

0.290

Gnomad4 AMR exome

AF:

0.0917

Gnomad4 ASJ exome

AF:

0.190

Gnomad4 EAS exome

AF:

0.114

Gnomad4 SAS exome

AF:

0.183

Gnomad4 FIN exome

AF:

0.249

Gnomad4 NFE exome

AF:

0.197

Gnomad4 OTH exome

AF:

0.187

GnomAD4 genome

AF:

0.219

AC:

33219

AN:

151924

Hom.:

3872

Cov.:

AF XY:

0.221

AC XY:

16400

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.289

Gnomad4 AMR

AF:

0.128

Gnomad4 ASJ

AF:

0.192

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.189

Gnomad4 FIN

AF:

0.261

Gnomad4 NFE

AF:

0.202

Gnomad4 OTH

AF:

0.192

Alfa

AF:

0.149

Hom.:

396

Bravo

AF:

0.211

Asia WGS

AF:

0.161

AC:

562

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.022

DANN

Benign

0.53

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