dbSNP rs9558575: DAOA-AS1:n.101-2134A>C (chr13-105494311-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000448407.1(DAOA-AS1):n.101-2134A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,106 control chromosomes in the GnomAD database, including 10,285 homozygotes. 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: 𝑓 0.34 ( 10285 hom., cov: 33)

Consequence

DAOA-AS1
ENST00000448407.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.619

Publications

2 publications found

Variant links:

Genes affected

DAOA-AS1 (HGNC:30243): (DAOA antisense RNA 1)

DAOA-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAOA-AS1	NR_040247.1 link	n.101-2134A>C		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAOA-AS1	ENST00000448407.1 link	n.101-2134A>C		intron_variant	Intron 1 of 6	2

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

51031

AN:

151988

Hom.:

10283

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.334

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.593

Gnomad SAS

AF:

0.543

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.400

Gnomad OTH

AF:

0.367

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.336

AC:

51039

AN:

152106

Hom.:

10285

Cov.:

AF XY:

0.346

AC XY:

25717

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.111

AC:

4622

AN:

41548

American (AMR)

AF:

0.417

AC:

6363

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.416

AC:

1441

AN:

3464

East Asian (EAS)

AF:

0.594

AC:

3064

AN:

5158

South Asian (SAS)

AF:

0.544

AC:

2623

AN:

4824

European-Finnish (FIN)

AF:

0.431

AC:

4546

AN:

10548

Middle Eastern (MID)

AF:

0.490

AC:

144

AN:

294

European-Non Finnish (NFE)

AF:

0.400

AC:

27162

AN:

67980

Other (OTH)

AF:

0.365

AC:

771

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1612

3224

4835

6447

8059

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

518

1036

1554

2072

2590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.361

Hom.:

1475

Bravo

AF:

0.319

Asia WGS

AF:

0.509

AC:

1768

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.8

(source)

DANN

Benign

0.30

PhyloP100

0.62

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