5-91428781-T-C

Position:

• chr5-91428781-T-C

Variant summary

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

The ENST00000701059.1(ARRDC3-AS1):​n.611+10010T>C 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 0.254 in 152,074 control chromosomes in the GnomAD database, including 6,105 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 0.25 (6105 hom., cov: 32)
• Consequence: ARRDC3-AS1 ENST00000701059.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 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+10010T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38638 AN: 151956 Hom.: 6087 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.254 AC: 38691 AN: 152074 Hom.: 6105 Cov.: 32 AF XY: 0.258 AC XY: 19154 AN XY: 74362

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.227

Alfa AF: 0.180 Hom.: 5872

Bravo AF: 0.262

Asia WGS AF: 0.444 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.38
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6862125; hg19: chr5-90724598;