5-91466931-G-A

Variant names:

• chr5-91466931-G-A
• rs933688
• ENST00000656345.1:n.474-3907G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 17 publications found

Genes affected

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

ENSG00000301415 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656345.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARRDC3-AS1	ENST00000656345.1		n.474-3907G>A		intron	N/A
	ARRDC3-AS1	ENST00000664873.1		n.139-3907G>A		intron	N/A
	ARRDC3-AS1	ENST00000690875.3		n.625-3907G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51204 AN: 151938 Hom.: 12870 Cov.: 32

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.: 32 AF XY: 0.337 AC XY: 25050 AN XY: 74342

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: 64 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10903 AN: 67976

Other (OTH) AF: 0.284 AC: 600 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.53
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs933688; hg19: chr5-90762748;