rs10474352

Variant names:

• chr5-91436408-C-T
• rs10474352
• ENST00000630823.3:n.592-2532C>T

Variant summary

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

The ENST00000630823.3(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 ENST00000630823.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 29 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=-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	ENST00000630823.3	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

African (AFR) AF: 0.350 AC: 14532 AN: 41476

American (AMR) AF: 0.202 AC: 3083 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3472

East Asian (EAS) AF: 0.490 AC: 2529 AN: 5166

South Asian (SAS) AF: 0.412 AC: 1985 AN: 4816

European-Finnish (FIN) AF: 0.131 AC: 1391 AN: 10590

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10670 AN: 68006

Other (OTH) AF: 0.215 AC: 454 AN: 2114

Alfa AF: 0.185 Hom.: 11126

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
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs10474352; hg19: chr5-90732225;