Variant 19-48298169-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.1404+8A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 1,610,912 control chromosomes in the GnomAD database, including 104,786 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 10563 hom., cov: 30)

Exomes 𝑓: 0.35 ( 94223 hom. )

Consequence

ODAD1
NM_001364171.2 splice_region, intron

Scores

Splicing: ADA: 0.00001091

Clinical Significance

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

Conservation

PhyloP100: -2.32

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=-0.95).

BP6

Variant 19-48298169-T-C is Benign according to our data. Variant chr19-48298169-T-C is described in ClinVar as [Benign]. Clinvar id is 262486.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 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.1404+8A>G		splice_region_variant, intron_variant		ENST00000674294.1
ODAD1	NM_144577.4 linkuse as main transcript	c.1293+8A>G		splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODAD1	ENST00000674294.1 linkuse as main transcript	c.1404+8A>G		splice_region_variant, intron_variant			NM_001364171.2	P2

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

55257

AN:

150932

Hom.:

10542

Cov.:

show subpopulations

Gnomad AFR

AF:

0.443

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.262

Gnomad ASJ

AF:

0.441

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.420

Gnomad NFE

AF:

0.369

Gnomad OTH

AF:

0.364

GnomAD3 exomes

AF:

0.318

AC:

79524

AN:

249742

Hom.:

13757

AF XY:

0.324

AC XY:

43765

AN XY:

135146

show subpopulations

Gnomad AFR exome

AF:

0.437

Gnomad AMR exome

AF:

0.175

Gnomad ASJ exome

AF:

0.442

Gnomad EAS exome

AF:

0.127

Gnomad SAS exome

AF:

0.294

Gnomad FIN exome

AF:

0.333

Gnomad NFE exome

AF:

0.368

Gnomad OTH exome

AF:

0.333

GnomAD4 exome

AF:

0.353

AC:

515679

AN:

1459860

Hom.:

94223

Cov.:

AF XY:

0.352

AC XY:

255473

AN XY:

726314

show subpopulations

Gnomad4 AFR exome

AF:

0.448

Gnomad4 AMR exome

AF:

0.186

Gnomad4 ASJ exome

AF:

0.443

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.290

Gnomad4 FIN exome

AF:

0.330

Gnomad4 NFE exome

AF:

0.369

Gnomad4 OTH exome

AF:

0.351

GnomAD4 genome

AF:

0.366

AC:

55313

AN:

151052

Hom.:

10563

Cov.:

AF XY:

0.360

AC XY:

26564

AN XY:

73724

show subpopulations

Gnomad4 AFR

AF:

0.443

Gnomad4 AMR

AF:

0.261

Gnomad4 ASJ

AF:

0.441

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.276

Gnomad4 FIN

AF:

0.337

Gnomad4 NFE

AF:

0.369

Gnomad4 OTH

AF:

0.363

Alfa

AF:

0.373

Hom.:

4598

Bravo

AF:

0.362

Asia WGS

AF:

0.212

AC:

743

AN:

3478

EpiCase

AF:

0.375

EpiControl

AF:

0.369

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 29, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Primary ciliary dyskinesia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.64

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000011

dbscSNV1_RF

Benign

0.0040

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