9-12682663-C-G

Variant names:

• chr9-12682663-C-G
• rs10809826
• ENST00000803542.1:n.310-51056G>C

Variant summary

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

The ENST00000803542.1(LURAP1L-AS1):​n.310-51056G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,930 control chromosomes in the GnomAD database, including 17,598 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 (17598 hom., cov: 31)
• Consequence: LURAP1L-AS1 ENST00000803542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803542.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LURAP1L-AS1	ENST00000803542.1		n.310-51056G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64855 AN: 151812 Hom.: 17599 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.427 AC: 64866 AN: 151930 Hom.: 17598 Cov.: 31 AF XY: 0.420 AC XY: 31183 AN XY: 74248

African (AFR) AF: 0.155 AC: 6437 AN: 41490

American (AMR) AF: 0.337 AC: 5127 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3468

East Asian (EAS) AF: 0.0167 AC: 86 AN: 5164

South Asian (SAS) AF: 0.219 AC: 1059 AN: 4828

European-Finnish (FIN) AF: 0.658 AC: 6941 AN: 10550

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42098 AN: 67892

Other (OTH) AF: 0.428 AC: 904 AN: 2110

Alfa AF: 0.399 Hom.: 1385

Bravo AF: 0.392

Asia WGS AF: 0.132 AC: 460 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10809826;

hg19: chr9-12682663;