11-119612120-C-T

Variant summary

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

The ENST00000706409.1(USP2-AS1):n.573-24805C>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 0.655 in 151,992 control chromosomes in the GnomAD database, including 32,825 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 0.66 (32825 hom., cov: 31)
• Consequence: USP2-AS1 ENST00000706409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742

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=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.681 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
USP2-AS1	ENST00000706409.1	n.573-24805C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99550 AN: 151874 Hom.: 32823 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.655 AC: 99594 AN: 151992 Hom.: 32825 Cov.: 31 AF XY: 0.652 AC XY: 48433 AN XY: 74272

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.676

Alfa AF: 0.674 Hom.: 5797

Bravo AF: 0.661

Asia WGS AF: 0.597 AC: 2079 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	0.40
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7949154; hg19: chr11-119482832;