dbSNP rs11015640: 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 ENST00000576034.6(ENSG00000262412):n.510T>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

ENSG00000262412
ENST00000576034.6 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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000576034.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ODAD2P1	NR_138082.1		n.505T>A		non_coding_transcript_exon	Exon 4 of 5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ODAD2P1	ENST00000438905.2	TSL:6	n.569T>A	non_coding_transcript_exon	Exon 4 of 4
ENSG00000262412	ENST00000576034.6	TSL:2	n.510T>A	non_coding_transcript_exon	Exon 4 of 5
ENSG00000262412	ENST00000787620.1		n.163T>A	non_coding_transcript_exon	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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over