11-119612120-C-T

Variant names:

• chr11-119612120-C-T
• rs7949154
• ENST00000706362.1:n.581-24805C>T

Variant summary

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

The ENST00000706362.1(USP2-AS1):​n.581-24805C>T variant causes a intron 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 ENST00000706362.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USP2-AS1	ENST00000706362.1	n.581-24805C>T		intron_variant	Intron 4 of 4
USP2-AS1	ENST00000706364.1	n.117+3581C>T		intron_variant	Intron 1 of 6
USP2-AS1	ENST00000706409.1	n.573-24805C>T		intron_variant	Intron 4 of 4

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;