rs1876794

Positions:

• chr11-119573305-C-G

Variant summary

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

The ENST00000706409.1(USP2-AS1):​n.572+29674C>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 0.554 in 151,694 control chromosomes in the GnomAD database, including 23,880 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 0.55 (23880 hom., cov: 29)
• Consequence: USP2-AS1 ENST00000706409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

Genes affected

USP2-AS1 (HGNC:48673): (USP2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 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
USP2-AS1	ENST00000706409.1	n.572+29674C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84077 AN: 151576 Hom.: 23888 Cov.: 29

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.554 AC: 84087 AN: 151694 Hom.: 23880 Cov.: 29 AF XY: 0.550 AC XY: 40739 AN XY: 74102

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.596

Alfa AF: 0.581 Hom.: 3236

Bravo AF: 0.553

Asia WGS AF: 0.499 AC: 1736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
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: rs1876794; hg19: chr11-119444016;