Genetic Variant ARRDC3-AS1:n.591+8446T>G (chr5-91427217-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 ENST00000630823.3(ARRDC3-AS1):n.591+8446T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,020 control chromosomes in the GnomAD database, including 11,565 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 0.32 ( 11565 hom., cov: 32)

Consequence

ARRDC3-AS1
ENST00000630823.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.799

Publications

8 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=-1.04).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ARRDC3-AS1	ENST00000630823.3 link	n.591+8446T>G	intron_variant	Intron 2 of 2	3
ARRDC3-AS1	ENST00000656345.1 link	n.473+8446T>G	intron_variant	Intron 2 of 3
ARRDC3-AS1	ENST00000664873.1 link	n.138+8446T>G	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49183

AN:

151902

Hom.:

11523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.648

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.525

Gnomad SAS

AF:

0.418

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.275

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

GnomAD4 genome

AF:

0.324

AC:

49286

AN:

152020

Hom.:

11565

Cov.:

AF XY:

0.325

AC XY:

24124

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.649

AC:

26875

AN:

41420

American (AMR)

AF:

0.255

AC:

3895

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.179

AC:

620

AN:

3466

East Asian (EAS)

AF:

0.526

AC:

2720

AN:

5172

South Asian (SAS)

AF:

0.419

AC:

2016

AN:

4814

European-Finnish (FIN)

AF:

0.136

AC:

1439

AN:

10584

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.161

AC:

10944

AN:

67972

Other (OTH)

AF:

0.277

AC:

585

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1361

2722

4084

5445

6806

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

448

896

1344

1792

2240

<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:

0.210

Hom.:

14990

Bravo

AF:

0.340

Asia WGS

AF:

0.458

AC:

1590

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

3.7

(source)

DANN

Benign

0.71

PhyloP100

-0.80

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