dbSNP rs933688: ARRDC3-AS1:n.474-3907G>A (chr5-91466931-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000656345.1(ARRDC3-AS1):n.474-3907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,056 control chromosomes in the GnomAD database, including 12,917 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 ( 12917 hom., cov: 32)

Consequence

ARRDC3-AS1
ENST00000656345.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0190

Publications

17 publications found

Variant links:

Genes affected

ARRDC3-AS1 (HGNC:44145): (ARRDC3 antisense RNA 1)

ARRDC3-AS1 links:

ENSG00000301415 (HGNC:):

ENSG00000301415 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ARRDC3-AS1	ENST00000656345.1 link	n.474-3907G>A	intron_variant	Intron 2 of 3
ARRDC3-AS1	ENST00000664873.1 link	n.139-3907G>A	intron_variant	Intron 2 of 4
ARRDC3-AS1	ENST00000690875.3 link	n.625-3907G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51204

AN:

151938

Hom.:

12870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.696

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.260

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.524

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.281

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

GnomAD4 genome

AF:

0.337

AC:

51313

AN:

152056

Hom.:

12917

Cov.:

AF XY:

0.337

AC XY:

25050

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.696

AC:

28863

AN:

41458

American (AMR)

AF:

0.260

AC:

3969

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

613

AN:

3470

East Asian (EAS)

AF:

0.525

AC:

2716

AN:

5172

South Asian (SAS)

AF:

0.421

AC:

2028

AN:

4814

European-Finnish (FIN)

AF:

0.135

AC:

1425

AN:

10580

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.160

AC:

10903

AN:

67976

Other (OTH)

AF:

0.284

AC:

600

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1315

2629

3944

5258

6573

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

456

912

1368

1824

2280

<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:

0.221

Hom.:

16504

Bravo

AF:

0.356

Asia WGS

AF:

0.463

AC:

1607

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.9

(source)

DANN

Benign

0.53

PhyloP100

0.019

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