rs145629439
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.808G>A(p.Asp270Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000784 in 1,614,204 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0010 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00076 ( 9 hom. )
Consequence
ODAD1
NM_001364171.2 missense
NM_001364171.2 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 2.74
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 (MetaRNN=0.010653675).
BP6
Variant 19-48303998-C-T is Benign according to our data. Variant chr19-48303998-C-T is described in ClinVar as [Benign]. Clinvar id is 413797.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00101 (154/152350) while in subpopulation EAS AF= 0.0128 (66/5174). AF 95% confidence interval is 0.0103. There are 0 homozygotes in gnomad4. There are 101 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ODAD1 | NM_001364171.2 | c.808G>A | p.Asp270Asn | missense_variant | 9/16 | ENST00000674294.1 | NP_001351100.1 | |
ODAD1 | NM_144577.4 | c.697G>A | p.Asp233Asn | missense_variant | 7/14 | NP_653178.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ODAD1 | ENST00000674294.1 | c.808G>A | p.Asp270Asn | missense_variant | 9/16 | NM_001364171.2 | ENSP00000501363 | P2 | ||
ODAD1 | ENST00000315396.7 | c.697G>A | p.Asp233Asn | missense_variant | 7/14 | 1 | ENSP00000318429 | A2 | ||
ODAD1 | ENST00000474199.6 | c.808G>A | p.Asp270Asn | missense_variant | 9/15 | 2 | ENSP00000501357 | A2 | ||
ODAD1 | ENST00000674207.1 | c.*516G>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/13 | ENSP00000501374 |
Frequencies
GnomAD3 genomes AF: 0.00101 AC: 154AN: 152232Hom.: 0 Cov.: 33
GnomAD3 genomes
AF:
AC:
154
AN:
152232
Hom.:
Cov.:
33
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: 0.00175 AC: 439AN: 251378Hom.: 5 AF XY: 0.00168 AC XY: 228AN XY: 135870
GnomAD3 exomes
AF:
AC:
439
AN:
251378
Hom.:
AF XY:
AC XY:
228
AN XY:
135870
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: 0.000761 AC: 1112AN: 1461854Hom.: 9 Cov.: 33 AF XY: 0.000765 AC XY: 556AN XY: 727232
GnomAD4 exome
AF:
AC:
1112
AN:
1461854
Hom.:
Cov.:
33
AF XY:
AC XY:
556
AN XY:
727232
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: 0.00101 AC: 154AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.00136 AC XY: 101AN XY: 74506
GnomAD4 genome
AF:
AC:
154
AN:
152350
Hom.:
Cov.:
33
AF XY:
AC XY:
101
AN XY:
74506
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:
ESP6500AA
AF:
AC:
0
ESP6500EA
AF:
AC:
4
ExAC
AF:
AC:
215
Asia WGS
AF:
AC:
2
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 11, 2021 | 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. - |
ODAD1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 03, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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