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GeneBe

19-11420734-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_145045.5(ODAD3):c.*101G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00951 in 1,023,654 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0078 ( 9 hom., cov: 31)
Exomes 𝑓: 0.0098 ( 52 hom. )

Consequence

ODAD3
NM_145045.5 3_prime_UTR

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.26
Variant links:
Genes affected
ODAD3 (HGNC:28303): (outer dynein arm docking complex subunit 3) This gene encodes a protein containing coiled-coil domains. The encoded protein functions in outer dynein arm assembly and is required for motile cilia function. Mutations in this gene result in primary ciliary dyskinesia. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 19-11420734-C-G is Benign according to our data. Variant chr19-11420734-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1215607.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00783 (1192/152326) while in subpopulation NFE AF= 0.0119 (810/68026). AF 95% confidence interval is 0.0112. There are 9 homozygotes in gnomad4. There are 564 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd at 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ODAD3NM_145045.5 linkuse as main transcriptc.*101G>C 3_prime_UTR_variant 13/13 ENST00000356392.9
ODAD3NM_001302453.1 linkuse as main transcriptc.*101G>C 3_prime_UTR_variant 13/13
ODAD3NM_001302454.2 linkuse as main transcriptc.*101G>C 3_prime_UTR_variant 11/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ODAD3ENST00000356392.9 linkuse as main transcriptc.*101G>C 3_prime_UTR_variant 13/131 NM_145045.5 P2A5D8V7-1
ODAD3ENST00000591179.5 linkuse as main transcriptc.*101G>C 3_prime_UTR_variant 11/111 A2
ODAD3ENST00000586836.5 linkuse as main transcriptc.*101G>C 3_prime_UTR_variant 13/132 A2
ODAD3ENST00000591345.5 linkuse as main transcriptc.*1808G>C 3_prime_UTR_variant, NMD_transcript_variant 14/145

Frequencies

GnomAD3 genomes
AF:
0.00784
AC:
1193
AN:
152208
Hom.:
9
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00268
Gnomad AMI
AF:
0.0351
Gnomad AMR
AF:
0.00334
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.0161
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0119
Gnomad OTH
AF:
0.00430
GnomAD4 exome
AF:
0.00980
AC:
8543
AN:
871328
Hom.:
52
Cov.:
12
AF XY:
0.00948
AC XY:
4260
AN XY:
449224
show subpopulations
Gnomad4 AFR exome
AF:
0.00210
Gnomad4 AMR exome
AF:
0.00197
Gnomad4 ASJ exome
AF:
0.000873
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00157
Gnomad4 FIN exome
AF:
0.0157
Gnomad4 NFE exome
AF:
0.0121
Gnomad4 OTH exome
AF:
0.00731
GnomAD4 genome
AF:
0.00783
AC:
1192
AN:
152326
Hom.:
9
Cov.:
31
AF XY:
0.00757
AC XY:
564
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.00267
Gnomad4 AMR
AF:
0.00333
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00124
Gnomad4 FIN
AF:
0.0161
Gnomad4 NFE
AF:
0.0119
Gnomad4 OTH
AF:
0.00426
Alfa
AF:
0.00294
Hom.:
0
Bravo
AF:
0.00657
Asia WGS
AF:
0.00144
AC:
5
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxJul 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
Cadd
Benign
0.75
Dann
Benign
0.35

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs370633080; hg19: chr19-11531402; API