chr5-91436408-C-T

Position:

• chr5-91436408-C-T

Variant summary

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

The ENST00000701059.1(ARRDC3-AS1):​n.611+17637C>T 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 0.233 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 ENST00000701059.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARRDC3-AS1	ENST00000701059.1	n.611+17637C>T		intron_variant, non_coding_transcript_variant

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;