11-119545617-G-T

Variant names:

• chr11-119545617-G-T
• rs925261
• ENST00000706362.2:n.580+1986G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000706362.2(USP2-AS1):​n.580+1986G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,158 control chromosomes in the GnomAD database, including 57,304 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 0.86 (57304 hom., cov: 31)
• Consequence: USP2-AS1 ENST00000706362.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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	ENST00000706362.2	n.580+1986G>T		intron_variant	Intron 4 of 4
USP2-AS1	ENST00000706409.1	n.572+1986G>T		intron_variant	Intron 4 of 4
USP2-AS1	ENST00000706415.2	n.416+1986G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130655 AN: 152040 Hom.: 57291 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.859 AC: 130712 AN: 152158 Hom.: 57304 Cov.: 31 AF XY: 0.862 AC XY: 64123 AN XY: 74416

African (AFR) AF: 0.660 AC: 27364 AN: 41432

American (AMR) AF: 0.928 AC: 14204 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3241 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5182 AN: 5190

South Asian (SAS) AF: 0.989 AC: 4779 AN: 4830

European-Finnish (FIN) AF: 0.893 AC: 9453 AN: 10590

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63490 AN: 68030

Other (OTH) AF: 0.894 AC: 1889 AN: 2112

Alfa AF: 0.879 Hom.: 3435

Bravo AF: 0.851

Asia WGS AF: 0.964 AC: 3351 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	0.54
DANN	Benign	0.36
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs925261; hg19: chr11-119416327;