rs10809814

Variant names:

• chr9-12659098-G-A
• rs10809814
• ENST00000803542.1:n.310-27491C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-12659098-G-A
• chr9-12659098-G-C
• chr9-12659098-G-T

Variant summary

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

The ENST00000803542.1(LURAP1L-AS1):​n.310-27491C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,088 control chromosomes in the GnomAD database, including 3,281 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 0.15 (3281 hom., cov: 32)
• Consequence: LURAP1L-AS1 ENST00000803542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LURAP1L-AS1	ENST00000803542.1	n.310-27491C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22717 AN: 151970 Hom.: 3266 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0546

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.150 AC: 22758 AN: 152088 Hom.: 3281 Cov.: 32 AF XY: 0.156 AC XY: 11630 AN XY: 74364

African (AFR) AF: 0.199 AC: 8262 AN: 41498

American (AMR) AF: 0.318 AC: 4865 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3470

East Asian (EAS) AF: 0.704 AC: 3600 AN: 5112

South Asian (SAS) AF: 0.149 AC: 717 AN: 4816

European-Finnish (FIN) AF: 0.0781 AC: 828 AN: 10608

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0546 AC: 3709 AN: 67982

Other (OTH) AF: 0.157 AC: 332 AN: 2110

Alfa AF: 0.138 Hom.: 843

Bravo AF: 0.177

Asia WGS AF: 0.426 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.46
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs10809814; hg19: chr9-12659098;