chr19-48296734-C-T

Position:

• chr19-48296734-C-T

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.*242G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 1,355,628 control chromosomes in the GnomAD database, including 739 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.042 (418 hom., cov: 32)
  • Exomes 𝑓: 0.0074 (321 hom.)
• Consequence: ODAD1 NM_001364171.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.02

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 19-48296734-C-T is Benign according to our data. Variant chr19-48296734-C-T is described in ClinVar as [Benign]. Clinvar id is 1247134.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODAD1	NM_001364171.2	c.*242G>A		3_prime_UTR_variant	16/16	ENST00000674294.1	NP_001351100.1
ODAD1	NM_144577.4	c.*242G>A		3_prime_UTR_variant	14/14		NP_653178.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODAD1	ENST00000674294	c.*242G>A		3_prime_UTR_variant	16/16		NM_001364171.2	ENSP00000501363.1

Frequencies

GnomAD3 genomes AF: 0.0421 AC: 6394 AN: 151930 Hom.: 417 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.000284

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00396

Gnomad OTH AF: 0.0283

GnomAD4 exome AF: 0.00741 AC: 8923 AN: 1203580 Hom.: 321 Cov.: 24 AF XY: 0.00723 AC XY: 4186 AN XY: 579214

Gnomad4 AFR exome AF: 0.149

Gnomad4 AMR exome AF: 0.0103

Gnomad4 ASJ exome AF: 0.00228

Gnomad4 EAS exome AF: 0.0000331

Gnomad4 SAS exome AF: 0.00836

Gnomad4 FIN exome AF: 0.000369

Gnomad4 NFE exome AF: 0.00395

Gnomad4 OTH exome AF: 0.0114

GnomAD4 genome AF: 0.0422 AC: 6411 AN: 152048 Hom.: 418 Cov.: 32 AF XY: 0.0414 AC XY: 3076 AN XY: 74312

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0149

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0106

Gnomad4 FIN AF: 0.000284

Gnomad4 NFE AF: 0.00396

Gnomad4 OTH AF: 0.0280

Alfa AF: 0.00478 Hom.: 8

Bravo AF: 0.0466

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 25, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.42

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

Other links and lift over

dbSNP: rs10413640; hg19: chr19-48799991;