rs34095

Positions:

• chr19-11430865-A-G

Variant summary

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

The NM_145045.5(ODAD3):​c.366+34T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,613,518 control chromosomes in the GnomAD database, including 244,440 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 0.62 (30156 hom., cov: 30)
  • Exomes 𝑓: 0.54 (214284 hom.)
• Consequence: ODAD3 NM_145045.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.088).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODAD3	NM_145045.5	c.366+34T>C		intron_variant		ENST00000356392.9
ODAD3	NM_001302453.1	c.204+34T>C		intron_variant
ODAD3	NM_001302454.2	c.366+34T>C		intron_variant
ODAD3	XM_017026241.2	c.366+34T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODAD3	ENST00000356392.9	c.366+34T>C		intron_variant		1	NM_145045.5	P2

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93821 AN: 151802 Hom.: 30102 Cov.: 30

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.607

GnomAD4 exome AF: 0.539 AC: 787611 AN: 1461598 Hom.: 214284 Cov.: 51 AF XY: 0.539 AC XY: 392227 AN XY: 727066

Gnomad4 AFR exome AF: 0.819

Gnomad4 AMR exome AF: 0.547

Gnomad4 ASJ exome AF: 0.575

Gnomad4 EAS exome AF: 0.464

Gnomad4 SAS exome AF: 0.584

Gnomad4 FIN exome AF: 0.585

Gnomad4 NFE exome AF: 0.525

Gnomad4 OTH exome AF: 0.563

GnomAD4 genome AF: 0.618 AC: 93935 AN: 151920 Hom.: 30156 Cov.: 30 AF XY: 0.617 AC XY: 45814 AN XY: 74230

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.610

Alfa AF: 0.542 Hom.: 18573

Bravo AF: 0.626

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.088

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34095; hg19: -;