5-91607792-A-G

Position:

• chr5-91607792-A-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The XR_007058864.1(LOC107986434):​n.3087A>G variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,694 control chromosomes in the GnomAD database, including 2,795 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 0.18 (2795 hom., cov: 32)
• Consequence: LOC107986434 XR_007058864.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.38

Genes affected

LOC107986434 (HGNC:):

ARRDC3-AS1 (HGNC:44145): (ARRDC3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986434	XR_007058864.1	n.3087A>G		non_coding_transcript_exon_variant	1/2
LOC107986434	XR_001742804.2	n.3040+47A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARRDC3-AS1	ENST00000701059.1	n.662-2905A>G		intron_variant, non_coding_transcript_variant
ARRDC3-AS1	ENST00000664205.1	n.190-2905A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27114 AN: 151578 Hom.: 2794 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0482

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.179 AC: 27118 AN: 151694 Hom.: 2795 Cov.: 32 AF XY: 0.180 AC XY: 13317 AN XY: 74108

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.0484

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.178

Alfa AF: 0.211 Hom.: 453

Bravo AF: 0.163

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	21
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514350; hg19: chr5-90903609;