rs13288636

chr9-12721807-G-A

Variant summary

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

The NR_125775.1(LURAP1L-AS1):n.317-21181C>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 0.429 in 151,986 control chromosomes in the GnomAD database, including 17,919 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 (17919 hom., cov: 32)
• Consequence: LURAP1L-AS1 NR_125775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

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=-0.93).
• 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	UniProt
LURAP1L-AS1	NR_125775.1	n.317-21181C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LURAP1L-AS1	ENST00000417638.1	n.273-21181C>T		intron_variant, non_coding_transcript_variant		3
LURAP1L-AS1	ENST00000650458.1	n.193-22452C>T		intron_variant, non_coding_transcript_variant
LURAP1L-AS1	ENST00000654076.1	n.159-21181C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65141 AN: 151870 Hom.: 17916 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: 0.640

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.429 AC: 65152 AN: 151986 Hom.: 17919 Cov.: 32 AF XY: 0.421 AC XY: 31302 AN XY: 74272

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: 0.640

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.441

Alfa AF: 0.539 Hom.: 5919

Bravo AF: 0.401

Asia WGS AF: 0.138 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	7.6
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13288636; hg19: chr9-12721806;