Genetic Variant ODAD2P1:n.569T>A (chr10-27288686-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000438905.2(ODAD2P1):n.569T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000206 in 1,307,998 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: 31)

Exomes 𝑓: 0.000021 ( 0 hom. )

Consequence

ODAD2P1
ENST00000438905.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.800

Publications

6 publications found

Variant links:

Genes affected

ODAD2P1 (HGNC:44937): (outer dynein arm docking complex subunit 2 pseudogene 1)

ODAD2P1 links:

ENSG00000262412 (HGNC:):

ENSG00000262412 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODAD2P1	NR_138082.1 link	n.505T>A		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ODAD2P1	ENST00000438905.2 link	n.569T>A	non_coding_transcript_exon_variant	Exon 4 of 4	6
ENSG00000262412	ENST00000576034.6 link	n.510T>A	non_coding_transcript_exon_variant	Exon 4 of 5	2
ENSG00000262412	ENST00000787620.1 link	n.163T>A	non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000206

AC:

AN:

1307998

Hom.:

Cov.:

AF XY:

0.0000199

AC XY:

AN XY:

653424

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

29698

American (AMR)

AF:

0.00

AC:

AN:

37708

Ashkenazi Jewish (ASJ)

AF:

0.0000437

AC:

AN:

22864

East Asian (EAS)

AF:

0.0000257

AC:

AN:

38862

South Asian (SAS)

AF:

0.00

AC:

AN:

75868

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51722

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5324

European-Non Finnish (NFE)

AF:

0.0000252

AC:

AN:

991196

Other (OTH)

AF:

0.00

AC:

AN:

54756

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

659

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.2

(source)

DANN

Benign

0.78

PhyloP100

0.80

Mutation Taster

=99/1

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over