rs13288681

Variant names:

• chr9-12721882-G-C
• rs13288681
• ENST00000417638.1:n.273-21256C>G

Variant summary

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

The ENST00000417638.1(LURAP1L-AS1):​n.273-21256C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,990 control chromosomes in the GnomAD database, including 17,851 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 0.43 (17851 hom., cov: 32)
• Consequence: LURAP1L-AS1 ENST00000417638.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769
• Publications: 5 publications found

Genes affected

LURAP1L-AS1 (HGNC:49761): (LURAP1L antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417638.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LURAP1L-AS1	NR_125775.1		n.317-21256C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LURAP1L-AS1	ENST00000417638.1	TSL:3	n.273-21256C>G		intron	N/A
	LURAP1L-AS1	ENST00000650458.1		n.193-22527C>G		intron	N/A
	LURAP1L-AS1	ENST00000654076.1		n.159-21256C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65032 AN: 151872 Hom.: 17848 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.428 AC: 65044 AN: 151990 Hom.: 17851 Cov.: 32 AF XY: 0.421 AC XY: 31254 AN XY: 74292

African (AFR) AF: 0.135 AC: 5591 AN: 41478

American (AMR) AF: 0.402 AC: 6139 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3470

East Asian (EAS) AF: 0.0198 AC: 102 AN: 5162

South Asian (SAS) AF: 0.228 AC: 1093 AN: 4804

European-Finnish (FIN) AF: 0.635 AC: 6712 AN: 10564

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42220 AN: 67934

Other (OTH) AF: 0.441 AC: 931 AN: 2112

Alfa AF: 0.527 Hom.: 2943

Bravo AF: 0.401

Asia WGS AF: 0.138 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.4
DANN	Benign	0.54
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs13288681; hg19: chr9-12721881;