Variant chr19-48302758-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001364171.2(ODAD1):c.1176G>A(p.Ser392=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 1,613,612 control chromosomes in the GnomAD database, including 6,019 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.060 ( 386 hom., cov: 32)

Exomes 𝑓: 0.082 ( 5633 hom. )

Consequence

ODAD1
NM_001364171.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -3.35

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 19-48302758-C-T is Benign according to our data. Variant chr19-48302758-C-T is described in ClinVar as [Benign]. Clinvar id is 262483.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.35 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0909 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.1176G>A	p.Ser392=	synonymous_variant	12/16	ENST00000674294.1
ODAD1	NM_144577.4 linkuse as main transcript	c.1065G>A	p.Ser355=	synonymous_variant	10/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODAD1	ENST00000674294.1 linkuse as main transcript	c.1176G>A	p.Ser392=	synonymous_variant	12/16		NM_001364171.2	P2

Frequencies

GnomAD3 genomes

AF:

0.0601

AC:

9146

AN:

152202

Hom.:

386

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0169

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.0669

Gnomad ASJ

AF:

0.0905

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0221

Gnomad FIN

AF:

0.0392

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0929

Gnomad OTH

AF:

0.0765

GnomAD3 exomes

AF:

0.0604

AC:

15094

AN:

249964

Hom.:

632

AF XY:

0.0609

AC XY:

8238

AN XY:

135278

show subpopulations

Gnomad AFR exome

AF:

0.0144

Gnomad AMR exome

AF:

0.0472

Gnomad ASJ exome

AF:

0.0940

Gnomad EAS exome

AF:

0.000327

Gnomad SAS exome

AF:

0.0239

Gnomad FIN exome

AF:

0.0399

Gnomad NFE exome

AF:

0.0909

Gnomad OTH exome

AF:

0.0734

GnomAD4 exome

AF:

0.0823

AC:

120296

AN:

1461292

Hom.:

5633

Cov.:

AF XY:

0.0805

AC XY:

58551

AN XY:

726974

show subpopulations

Gnomad4 AFR exome

AF:

0.0122

Gnomad4 AMR exome

AF:

0.0502

Gnomad4 ASJ exome

AF:

0.0946

Gnomad4 EAS exome

AF:

0.000176

Gnomad4 SAS exome

AF:

0.0242

Gnomad4 FIN exome

AF:

0.0412

Gnomad4 NFE exome

AF:

0.0950

Gnomad4 OTH exome

AF:

0.0827

GnomAD4 genome

AF:

0.0600

AC:

9143

AN:

152320

Hom.:

386

Cov.:

AF XY:

0.0573

AC XY:

4269

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.0168

Gnomad4 AMR

AF:

0.0668

Gnomad4 ASJ

AF:

0.0905

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0223

Gnomad4 FIN

AF:

0.0392

Gnomad4 NFE

AF:

0.0929

Gnomad4 OTH

AF:

0.0757

Alfa

AF:

0.0821

Hom.:

332

Bravo

AF:

0.0603

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.0966

EpiControl

AF:

0.0963

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Primary ciliary dyskinesia

Benign:2

Benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 07, 2016	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 27, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.12

DANN

Benign

0.57

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over