rs112569880
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001364171.2(ODAD1):c.988+11C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00134 in 1,613,942 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0070 ( 17 hom., cov: 32)
Exomes 𝑓: 0.00075 ( 18 hom. )
Consequence
ODAD1
NM_001364171.2 intron
NM_001364171.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.495
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 19-48303639-G-T is Benign according to our data. Variant chr19-48303639-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 262508.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00704 (1071/152196) while in subpopulation AFR AF= 0.0243 (1007/41516). AF 95% confidence interval is 0.023. There are 17 homozygotes in gnomad4. There are 518 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 17 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ODAD1 | ENST00000674294.1 | c.988+11C>A | intron_variant | NM_001364171.2 | ENSP00000501363.1 | |||||
ODAD1 | ENST00000315396.7 | c.877+11C>A | intron_variant | 1 | ENSP00000318429.7 | |||||
ODAD1 | ENST00000474199.6 | c.988+11C>A | intron_variant | 2 | ENSP00000501357.1 | |||||
ODAD1 | ENST00000674207.1 | n.*696+11C>A | intron_variant | ENSP00000501374.1 |
Frequencies
GnomAD3 genomes AF: 0.00696 AC: 1059AN: 152078Hom.: 17 Cov.: 32
GnomAD3 genomes
AF:
AC:
1059
AN:
152078
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00195 AC: 490AN: 251194Hom.: 7 AF XY: 0.00131 AC XY: 178AN XY: 135752
GnomAD3 exomes
AF:
AC:
490
AN:
251194
Hom.:
AF XY:
AC XY:
178
AN XY:
135752
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000748 AC: 1093AN: 1461746Hom.: 18 Cov.: 32 AF XY: 0.000609 AC XY: 443AN XY: 727178
GnomAD4 exome
AF:
AC:
1093
AN:
1461746
Hom.:
Cov.:
32
AF XY:
AC XY:
443
AN XY:
727178
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00704 AC: 1071AN: 152196Hom.: 17 Cov.: 32 AF XY: 0.00696 AC XY: 518AN XY: 74400
GnomAD4 genome
AF:
AC:
1071
AN:
152196
Hom.:
Cov.:
32
AF XY:
AC XY:
518
AN XY:
74400
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
17
AN:
3478
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Primary ciliary dyskinesia Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 13, 2025 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 19, 2021 | See Variant Classification Assertion Criteria. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at