GeneBe

19-48296984-G-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_001364171.2(ODAD1):​c.2116C>A​(p.Arg706Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,448,594 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

ODAD1
NM_001364171.2 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0190

Publications

0 publications found
Variant links:
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

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP7
Synonymous conserved (PhyloP=-0.019 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ODAD1NM_001364171.2 linkc.2116C>A p.Arg706Arg synonymous_variant Exon 16 of 16 ENST00000674294.1 NP_001351100.1
ODAD1NM_144577.4 linkc.2005C>A p.Arg669Arg synonymous_variant Exon 14 of 14 NP_653178.3 Q96M63-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ODAD1ENST00000674294.1 linkc.2116C>A p.Arg706Arg synonymous_variant Exon 16 of 16 NM_001364171.2 ENSP00000501363.1 A0A6I8PTZ2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.90e-7
AC:
1
AN:
1448594
Hom.:
0
Cov.:
32
AF XY:
0.00000139
AC XY:
1
AN XY:
720022
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
33292
American (AMR)
AF:
0.00
AC:
0
AN:
43986
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25278
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39620
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85032
European-Finnish (FIN)
AF:
0.0000199
AC:
1
AN:
50180
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4542
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1106882
Other (OTH)
AF:
0.00
AC:
0
AN:
59782
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
2.0
DANN
Benign
0.57
PhyloP100
-0.019

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

Other links and lift over

dbSNP: rs200369693; hg19: chr19-48800241; API