rs2382360

Positions:

• chr9-12710413-T-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.317-9787A>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 0.157 in 151,298 control chromosomes in the GnomAD database, including 2,071 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 0.16 (2071 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: LURAP1L-AS1 NR_125775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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 (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LURAP1L-AS1	NR_125775.1	n.317-9787A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LURAP1L-AS1	ENST00000417638.1	n.273-9787A>G		intron_variant, non_coding_transcript_variant		3
LURAP1L-AS1	ENST00000650458.1	n.193-11058A>G		intron_variant, non_coding_transcript_variant
LURAP1L-AS1	ENST00000654076.1	n.159-9787A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23772 AN: 151176 Hom.: 2075 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0931

Gnomad MID AF: 0.262

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.157 AC: 23778 AN: 151298 Hom.: 2071 Cov.: 31 AF XY: 0.154 AC XY: 11412 AN XY: 73910

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0931

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.187

Alfa AF: 0.144 Hom.: 373

Bravo AF: 0.163

Asia WGS AF: 0.170 AC: 585 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.47
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2382360; hg19: chr9-12710413; COSMIC: COSV66358424;