rs41306079

chr9-12710473-T-G

Variant summary

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

The NR_125775.1(LURAP1L-AS1):n.317-9847A>C 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 0.119 in 151,320 control chromosomes in the GnomAD database, including 1,321 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 0.12 (1321 hom., cov: 31)
• Consequence: LURAP1L-AS1 NR_125775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.632

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LURAP1L-AS1	NR_125775.1	n.317-9847A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LURAP1L-AS1	ENST00000417638.1	n.273-9847A>C		intron_variant, non_coding_transcript_variant		3
LURAP1L-AS1	ENST00000650458.1	n.193-11118A>C		intron_variant, non_coding_transcript_variant
LURAP1L-AS1	ENST00000654076.1	n.159-9847A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18015 AN: 151206 Hom.: 1317 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.0856

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.119 AC: 18041 AN: 151320 Hom.: 1321 Cov.: 31 AF XY: 0.119 AC XY: 8768 AN XY: 73934

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.0858

Gnomad4 SAS AF: 0.0763

Gnomad4 FIN AF: 0.0768

Gnomad4 NFE AF: 0.0854

Gnomad4 OTH AF: 0.112

Alfa AF: 0.105 Hom.: 121

Bravo AF: 0.124

Asia WGS AF: 0.0860 AC: 295 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	12
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41306079; hg19: chr9-12710473;