19-48298157-G-T

Variant names:

• chr19-48298157-G-T
• rs8111297
• NM_001364171.2:c.1404+20C>A

Variant summary

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

The NM_001364171.2(ODAD1):​c.1404+20C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,611,326 control chromosomes in the GnomAD database, including 29,113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.18 (2514 hom., cov: 31)
  • Exomes 𝑓: 0.19 (26599 hom.)
• Consequence: ODAD1 NM_001364171.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -2.72
• Publications: 6 publications found

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]

ODAD1 Gene-Disease associations (from GenCC):

• primary ciliary dyskinesia 20

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

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 19-48298157-G-T is Benign according to our data. Variant chr19-48298157-G-T is described in ClinVar as Benign. ClinVar VariationId is 262485.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODAD1	NM_001364171.2	c.1404+20C>A		intron_variant	Intron 13 of 15	ENST00000674294.1	NP_001351100.1
ODAD1	NM_144577.4	c.1293+20C>A		intron_variant	Intron 11 of 13		NP_653178.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODAD1	ENST00000674294.1	c.1404+20C>A		intron_variant	Intron 13 of 15		NM_001364171.2	ENSP00000501363.1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 26945 AN: 151666 Hom.: 2512 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.169

GnomAD2 exomes AF: 0.177 AC: 44188 AN: 249520 AF XY: 0.183

Gnomad AFR exome AF: 0.154

Gnomad AMR exome AF: 0.0837

Gnomad ASJ exome AF: 0.185

Gnomad EAS exome AF: 0.126

Gnomad FIN exome AF: 0.261

Gnomad NFE exome AF: 0.200

Gnomad OTH exome AF: 0.171

GnomAD4 exome AF: 0.187 AC: 272823 AN: 1459542 Hom.: 26599 Cov.: 35 AF XY: 0.188 AC XY: 136307 AN XY: 726144

African (AFR) AF: 0.153 AC: 5108 AN: 33466

American (AMR) AF: 0.0869 AC: 3886 AN: 44706

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 4711 AN: 26116

East Asian (EAS) AF: 0.115 AC: 4564 AN: 39694

South Asian (SAS) AF: 0.177 AC: 15273 AN: 86238

European-Finnish (FIN) AF: 0.252 AC: 13042 AN: 51662

Middle Eastern (MID) AF: 0.183 AC: 1056 AN: 5768

European-Non Finnish (NFE) AF: 0.193 AC: 214588 AN: 1111534

Other (OTH) AF: 0.176 AC: 10595 AN: 60358

GnomAD4 genome AF: 0.178 AC: 26947 AN: 151784 Hom.: 2514 Cov.: 31 AF XY: 0.180 AC XY: 13329 AN XY: 74148

African (AFR) AF: 0.156 AC: 6447 AN: 41384

American (AMR) AF: 0.114 AC: 1740 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3470

East Asian (EAS) AF: 0.124 AC: 636 AN: 5116

South Asian (SAS) AF: 0.176 AC: 844 AN: 4800

European-Finnish (FIN) AF: 0.260 AC: 2746 AN: 10556

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.197 AC: 13382 AN: 67888

Other (OTH) AF: 0.170 AC: 358 AN: 2108

Alfa AF: 0.136 Hom.: 337

Bravo AF: 0.167

Asia WGS AF: 0.149 AC: 521 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

not specified Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Primary ciliary dyskinesia Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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	-0.91
CADD	Benign	0.040
DANN	Benign	0.44
PhyloP100		-2.7
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: rs8111297; hg19: chr19-48801414; COSMIC: COSV59557446;