19-11430892-C-T

Position:

• chr19-11430892-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145045.5(ODAD3):​c.366+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0225 in 1,613,976 control chromosomes in the GnomAD database, including 1,862 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.065 (807 hom., cov: 30)
  • Exomes 𝑓: 0.018 (1055 hom.)
• Consequence: ODAD3 NM_145045.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

Genes affected

ODAD3 (HGNC:28303): (outer dynein arm docking complex subunit 3) This gene encodes a protein containing coiled-coil domains. The encoded protein functions in outer dynein arm assembly and is required for motile cilia function. Mutations in this gene result in primary ciliary dyskinesia. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]

ODAD3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=1.288).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ODAD3	NM_145045.5	c.366+7G>A		splice_region_variant, intron_variant		ENST00000356392.9	NP_659482.3
ODAD3	NM_001302453.1	c.204+7G>A		splice_region_variant, intron_variant			NP_001289382.1
ODAD3	NM_001302454.2	c.366+7G>A		splice_region_variant, intron_variant			NP_001289383.1
ODAD3	XM_017026241.2	c.366+7G>A		splice_region_variant, intron_variant			XP_016881730.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ODAD3	ENST00000356392.9	c.366+7G>A		splice_region_variant, intron_variant		1	NM_145045.5	ENSP00000348757.3

Frequencies

GnomAD3 genomes AF: 0.0651 AC: 9891 AN: 152028 Hom.: 804 Cov.: 30

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0332

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0257

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00937

Gnomad OTH AF: 0.0578

GnomAD4 exome AF: 0.0181 AC: 26460 AN: 1461830 Hom.: 1055 Cov.: 35 AF XY: 0.0180 AC XY: 13079 AN XY: 727202

Gnomad4 AFR exome AF: 0.186

Gnomad4 AMR exome AF: 0.0172

Gnomad4 ASJ exome AF: 0.0141

Gnomad4 EAS exome AF: 0.101

Gnomad4 SAS exome AF: 0.0303

Gnomad4 FIN exome AF: 0.0254

Gnomad4 NFE exome AF: 0.00806

Gnomad4 OTH exome AF: 0.0335

GnomAD4 genome AF: 0.0652 AC: 9918 AN: 152146 Hom.: 807 Cov.: 30 AF XY: 0.0639 AC XY: 4757 AN XY: 74398

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.0331

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.0305

Gnomad4 FIN AF: 0.0257

Gnomad4 NFE AF: 0.00937

Gnomad4 OTH AF: 0.0581

Alfa AF: 0.0212 Hom.: 256

Bravo AF: 0.0705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34094; hg19: -;