rs3808909

Variant names:

• chr10-27987344-G-A
• rs3808909
• NM_018076.5:c.382+42C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-27987344-G-A
• chr10-27987344-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_018076.5(ODAD2):​c.382+42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 1,578,882 control chromosomes in the GnomAD database, including 46,159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.20 (3500 hom., cov: 32)
  • Exomes 𝑓: 0.24 (42659 hom.)
• Consequence: ODAD2 NM_018076.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.31
• Publications: 7 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: ClinGen, G2P, Labcorp Genetics (formerly Invitae)
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

LOC112268060 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 10-27987344-G-A is Benign according to our data. Variant chr10-27987344-G-A is described in ClinVar as Benign. ClinVar VariationId is 1235317.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018076.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODAD2	NM_018076.5	MANE Select	c.382+42C>T		intron	N/A	NP_060546.2
	ODAD2	NM_001290020.2		c.382+42C>T		intron	N/A	NP_001276949.1	A0A140VKF7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODAD2	ENST00000305242.10	TSL:1 MANE Select	c.382+42C>T		intron	N/A	ENSP00000306410.5	Q5T2S8-1
	ODAD2	ENST00000673439.1		c.382+42C>T		intron	N/A	ENSP00000500782.1	Q5T2S8-1
	ODAD2	ENST00000852623.1		c.382+42C>T		intron	N/A	ENSP00000522682.1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30334 AN: 151964 Hom.: 3498 Cov.: 32

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.213

GnomAD2 exomes AF: 0.222 AC: 52818 AN: 237868 AF XY: 0.225

Gnomad AFR exome AF: 0.0994

Gnomad AMR exome AF: 0.262

Gnomad ASJ exome AF: 0.201

Gnomad EAS exome AF: 0.0530

Gnomad FIN exome AF: 0.288

Gnomad NFE exome AF: 0.250

Gnomad OTH exome AF: 0.237

GnomAD4 exome AF: 0.240 AC: 341836 AN: 1426800 Hom.: 42659 Cov.: 26 AF XY: 0.239 AC XY: 169402 AN XY: 707956

African (AFR) AF: 0.0962 AC: 3115 AN: 32366

American (AMR) AF: 0.260 AC: 10629 AN: 40910

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 4807 AN: 24984

East Asian (EAS) AF: 0.0617 AC: 2427 AN: 39366

South Asian (SAS) AF: 0.208 AC: 16835 AN: 81048

European-Finnish (FIN) AF: 0.282 AC: 14868 AN: 52636

Middle Eastern (MID) AF: 0.260 AC: 1464 AN: 5624

European-Non Finnish (NFE) AF: 0.252 AC: 274635 AN: 1090930

Other (OTH) AF: 0.222 AC: 13056 AN: 58936

GnomAD4 genome AF: 0.199 AC: 30332 AN: 152082 Hom.: 3500 Cov.: 32 AF XY: 0.201 AC XY: 14973 AN XY: 74316

African (AFR) AF: 0.0981 AC: 4071 AN: 41508

American (AMR) AF: 0.243 AC: 3703 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3470

East Asian (EAS) AF: 0.0578 AC: 299 AN: 5176

South Asian (SAS) AF: 0.197 AC: 948 AN: 4820

European-Finnish (FIN) AF: 0.279 AC: 2946 AN: 10544

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16964 AN: 67976

Other (OTH) AF: 0.211 AC: 445 AN: 2112

Alfa AF: 0.222 Hom.: 1075

Bravo AF: 0.193

Asia WGS AF: 0.118 AC: 412 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.35
DANN	Benign	0.36
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3808909; hg19: chr10-28276273;