5-91427217-T-G

Position:

• chr5-91427217-T-G

Variant summary

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

The ENST00000701059.1(ARRDC3-AS1):​n.611+8446T>G 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 0.324 in 152,020 control chromosomes in the GnomAD database, including 11,565 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 0.32 (11565 hom., cov: 32)
• Consequence: ARRDC3-AS1 ENST00000701059.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARRDC3-AS1	ENST00000701059.1	n.611+8446T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49183 AN: 151902 Hom.: 11523 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.324 AC: 49286 AN: 152020 Hom.: 11565 Cov.: 32 AF XY: 0.325 AC XY: 24124 AN XY: 74316

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.277

Alfa AF: 0.184 Hom.: 4742

Bravo AF: 0.340

Asia WGS AF: 0.458 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6452953; hg19: chr5-90723034;