rs933688

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000701059.1(ARRDC3-AS1):​n.612-3907G>A variant causes a intron, non coding transcript 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 ENST00000701059.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARRDC3-AS1	ENST00000701059.1	n.612-3907G>A		intron_variant, non_coding_transcript_variant
ARRDC3-AS1	ENST00000656345.1	n.474-3907G>A		intron_variant, non_coding_transcript_variant
ARRDC3-AS1	ENST00000664873.1	n.139-3907G>A		intron_variant, non_coding_transcript_variant
ARRDC3-AS1	ENST00000690875.2	n.612-3907G>A		intron_variant, non_coding_transcript_variant

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;