rs10474352

Variant names:

• chr5-91436408-C-T
• rs10474352
• ENST00000630823.2:n.592-2532C>T

Variant summary

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

The ENST00000630823.2(ARRDC3-AS1):​n.592-2532C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,122 control chromosomes in the GnomAD database, including 4,939 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 0.23 (4939 hom., cov: 32)
• Consequence: ARRDC3-AS1 ENST00000630823.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 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	ENST00000630823.2	n.592-2532C>T		intron_variant	Intron 2 of 2	3
ARRDC3-AS1	ENST00000656345.1	n.473+17637C>T		intron_variant	Intron 2 of 3
ARRDC3-AS1	ENST00000664873.1	n.138+17637C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35377 AN: 152004 Hom.: 4928 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.233 AC: 35417 AN: 152122 Hom.: 4939 Cov.: 32 AF XY: 0.235 AC XY: 17486 AN XY: 74352

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.215

Alfa AF: 0.170 Hom.: 4037

Bravo AF: 0.237

Asia WGS AF: 0.418 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10474352; hg19: chr5-90732225;