rs13288681

Positions:

• chr9-12721882-G-C

Variant summary

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

The NR_125775.1(LURAP1L-AS1):​n.317-21256C>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 0.428 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 NR_125775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LURAP1L-AS1	NR_125775.1	n.317-21256C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LURAP1L-AS1	ENST00000417638.1	n.273-21256C>G		intron_variant, non_coding_transcript_variant		3
LURAP1L-AS1	ENST00000650458.1	n.193-22527C>G		intron_variant, non_coding_transcript_variant
LURAP1L-AS1	ENST00000654076.1	n.159-21256C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.0198

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.441

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13288681; hg19: chr9-12721881;