rs34091

Positions:

• chr19-11431541-T-A
• chr19-11431541-T-C

Variant summary

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

The NM_145045.5(ODAD3):​c.245-521A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 151,234 control chromosomes in the GnomAD database, including 2,705 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 0.16 (2705 hom., cov: 28)
• Consequence: ODAD3 NM_145045.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

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 (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ODAD3	NM_145045.5	c.245-521A>T		intron_variant		ENST00000356392.9
ODAD3	NM_001302453.1	c.83-521A>T		intron_variant
ODAD3	NM_001302454.2	c.245-521A>T		intron_variant
ODAD3	XM_017026241.2	c.245-521A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ODAD3	ENST00000356392.9	c.245-521A>T		intron_variant		1	NM_145045.5	P2

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23499 AN: 151118 Hom.: 2692 Cov.: 28

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0972

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.150

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.156 AC: 23557 AN: 151234 Hom.: 2705 Cov.: 28 AF XY: 0.156 AC XY: 11501 AN XY: 73840

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.0972

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0710

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0705

Gnomad4 OTH AF: 0.149

Alfa AF: 0.116 Hom.: 208

Bravo AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
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: rs34091; hg19: chr19-11542361;