rs2815496

Variant names:

• chr10-27792359-C-A
• rs2815496
• ENST00000673384.1:n.*128+3981G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-27792359-C-A
• chr10-27792359-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000673384.1(ODAD2):​n.*128+3981G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,872 control chromosomes in the GnomAD database, including 14,409 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 0.41 (14409 hom., cov: 32)
• Consequence: ODAD2 ENST00000673384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 2 publications found

Genes affected

ODAD2 (HGNC:25583): (outer dynein arm docking complex subunit 2) The protein encoded by this gene contains ten Armadillo repeat motifs (ARMs) and one HEAT repeat, and is thought to be involved in ciliary and flagellar movement. This protein has been shown to localize to the ciliary axonemes and at the ciliary base of respiratory cells. Studies indicate that mutations in this gene cause partial outer dynein arm (ODA) defects in respiratory cilia. The cilia of cells with mutations in this gene displayed either reduced ciliary beat frequency and amplitude, or, complete immotility. Some individuals with primary ciliary dyskensia (PCD) have been shown to have mutations in this gene. PCD is characterized by chronic airway disease and left/right body asymmetry defects. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]

ODAD2 Gene-Disease associations (from GenCC):

• primary ciliary dyskinesia 23

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae)
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODAD2	ENST00000673384.1	n.*128+3981G>T		intron_variant	Intron 16 of 17			ENSP00000500856.1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61711 AN: 151754 Hom.: 14407 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.406 AC: 61724 AN: 151872 Hom.: 14409 Cov.: 32 AF XY: 0.401 AC XY: 29731 AN XY: 74212

African (AFR) AF: 0.190 AC: 7858 AN: 41342

American (AMR) AF: 0.375 AC: 5730 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1536 AN: 5176

South Asian (SAS) AF: 0.386 AC: 1862 AN: 4820

European-Finnish (FIN) AF: 0.414 AC: 4368 AN: 10552

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36862 AN: 67940

Other (OTH) AF: 0.431 AC: 909 AN: 2110

Alfa AF: 0.487 Hom.: 15692

Bravo AF: 0.392

Asia WGS AF: 0.328 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.77
DANN	Benign	0.85
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2815496; hg19: chr10-28081288;