Variant chr19-48297534-A-G 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.1582-16T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 1,595,706 control chromosomes in the GnomAD database, including 106,701 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 11386 hom., cov: 31)

Exomes 𝑓: 0.36 ( 95315 hom. )

Consequence

ODAD1
NM_001364171.2 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.109

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=-0.97).

BP6

Variant 19-48297534-A-G is Benign according to our data. Variant chr19-48297534-A-G is described in ClinVar as [Benign]. Clinvar id is 262490.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODAD1	NM_001364171.2 linkuse as main transcript	c.1582-16T>C		splice_polypyrimidine_tract_variant, intron_variant		ENST00000674294.1	NP_001351100.1
ODAD1	NM_144577.4 linkuse as main transcript	c.1471-16T>C		splice_polypyrimidine_tract_variant, intron_variant			NP_653178.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODAD1	ENST00000674294.1 linkuse as main transcript	c.1582-16T>C		splice_polypyrimidine_tract_variant, intron_variant			NM_001364171.2	ENSP00000501363	P2

Frequencies

GnomAD3 genomes

AF:

0.378

AC:

57281

AN:

151694

Hom.:

11365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.445

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.369

GnomAD3 exomes

AF:

0.319

AC:

69275

AN:

217314

Hom.:

11933

AF XY:

0.324

AC XY:

38244

AN XY:

118160

show subpopulations

Gnomad AFR exome

AF:

0.477

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.438

Gnomad EAS exome

AF:

0.125

Gnomad SAS exome

AF:

0.298

Gnomad FIN exome

AF:

0.331

Gnomad NFE exome

AF:

0.369

Gnomad OTH exome

AF:

0.334

GnomAD4 exome

AF:

0.357

AC:

515596

AN:

1443896

Hom.:

95315

Cov.:

AF XY:

0.355

AC XY:

254917

AN XY:

717206

show subpopulations

Gnomad4 AFR exome

AF:

0.489

Gnomad4 AMR exome

AF:

0.188

Gnomad4 ASJ exome

AF:

0.442

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.297

Gnomad4 FIN exome

AF:

0.329

Gnomad4 NFE exome

AF:

0.372

Gnomad4 OTH exome

AF:

0.356

GnomAD4 genome

AF:

0.378

AC:

57341

AN:

151810

Hom.:

11386

Cov.:

AF XY:

0.371

AC XY:

27538

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.479

Gnomad4 AMR

AF:

0.265

Gnomad4 ASJ

AF:

0.445

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.286

Gnomad4 FIN

AF:

0.333

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.368

Alfa

AF:

0.385

Hom.:

2104

Bravo

AF:

0.377

Asia WGS

AF:

0.220

AC:

769

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

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	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

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

-0.97

CADD

Benign

8.0

DANN

Benign

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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