19-48296961-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.87

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]

ACMG classification

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	c.*15A>G		3_prime_UTR_variant	16/16	ENST00000674294.1
ODAD1	NM_144577.4	c.*15A>G		3_prime_UTR_variant	14/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODAD1	ENST00000674294.1	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.: 31

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

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.: 32 AF XY: 0.194 AC XY: 136349 AN XY: 701862

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.: 31 AF XY: 0.221 AC XY: 16400 AN XY: 74266

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

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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- -

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

Other links and lift over

dbSNP: rs10415825; hg19: chr19-48800218;