rs933688

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-91466931-G-A
• chr5-91466931-G-C
• chr5-91466931-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARRDC3-AS1	ENST00000656345.1	n.474-3907G>A		intron_variant	Intron 2 of 3
ARRDC3-AS1	ENST00000664873.1	n.139-3907G>A		intron_variant	Intron 2 of 4
ARRDC3-AS1	ENST00000690875.2	n.612-3907G>A		intron_variant	Intron 2 of 2
ARRDC3-AS1	ENST00000701059.1	n.612-3907G>A		intron_variant	Intron 2 of 4

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

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.284

Alfa AF: 0.188 Hom.: 6627

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
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs933688; hg19: chr5-90762748;