rs28582401

Variant names:

• chr19-48304110-C-A
• rs28582401
• NM_001364171.2:c.696G>T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_001364171.2(ODAD1):​c.696G>T​(p.Leu232Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,611,918 control chromosomes in the GnomAD database, including 29,165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.18 (2536 hom., cov: 33)
  • Exomes 𝑓: 0.19 (26629 hom.)
• Consequence: ODAD1 NM_001364171.2 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: 0.206

Genes affected

ODAD1 (HGNC:26560): (outer dynein arm docking complex subunit 1) This gene encodes a coiled-coil domain-containing protein that is a component of the outer dynein arm docking complex in cilia cells. Mutations in this gene may cause primary ciliary dyskinesia 20. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Benign. Variant got -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BP6: Variant 19-48304110-C-A is Benign according to our data. Variant chr19-48304110-C-A is described in ClinVar as [Benign]. Clinvar id is 262504.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.206 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODAD1	NM_001364171.2	c.696G>T	p.Leu232Leu	synonymous_variant	Exon 9 of 16	ENST00000674294.1	NP_001351100.1
ODAD1	NM_144577.4	c.585G>T	p.Leu195Leu	synonymous_variant	Exon 7 of 14		NP_653178.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODAD1	ENST00000674294.1	c.696G>T	p.Leu232Leu	synonymous_variant	Exon 9 of 16		NM_001364171.2	ENSP00000501363.1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27146 AN: 152066 Hom.: 2534 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.168

GnomAD3 exomes AF: 0.178 AC: 44368 AN: 249752 Hom.: 4293 AF XY: 0.183 AC XY: 24716 AN XY: 135108

Gnomad AFR exome AF: 0.158

Gnomad AMR exome AF: 0.0839

Gnomad ASJ exome AF: 0.185

Gnomad EAS exome AF: 0.127

Gnomad SAS exome AF: 0.181

Gnomad FIN exome AF: 0.262

Gnomad NFE exome AF: 0.200

Gnomad OTH exome AF: 0.172

GnomAD4 exome AF: 0.187 AC: 273169 AN: 1459734 Hom.: 26629 Cov.: 35 AF XY: 0.188 AC XY: 136349 AN XY: 725938

Gnomad4 AFR exome AF: 0.157

Gnomad4 AMR exome AF: 0.0873

Gnomad4 ASJ exome AF: 0.180

Gnomad4 EAS exome AF: 0.115

Gnomad4 SAS exome AF: 0.175

Gnomad4 FIN exome AF: 0.254

Gnomad4 NFE exome AF: 0.193

Gnomad4 OTH exome AF: 0.176

GnomAD4 genome AF: 0.178 AC: 27152 AN: 152184 Hom.: 2536 Cov.: 33 AF XY: 0.181 AC XY: 13439 AN XY: 74400

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.169

Alfa AF: 0.186 Hom.: 1149

Bravo AF: 0.168

Asia WGS AF: 0.151 AC: 527 AN: 3478

EpiCase AF: 0.189

EpiControl AF: 0.185

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Primary ciliary dyskinesia Benign:2

Jul 09, 2016

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 22, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Benign:1

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	4.6
DANN	Benign	0.81

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

Publications

LitVar

Other links and lift over

dbSNP: rs28582401; hg19: chr19-48807367; COSMIC: COSV59557783; COSMIC: COSV59557783;