rs1408799

Variant names:

• chr9-12672097-T-C
• rs1408799
• ENST00000803542.1:n.310-40490A>G

Variant summary

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

The ENST00000803542.1(LURAP1L-AS1):​n.310-40490A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,638 control chromosomes in the GnomAD database, including 22,910 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 0.51 (22910 hom., cov: 32)
• Consequence: LURAP1L-AS1 ENST00000803542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 75 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 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.310-40490A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76584 AN: 151520 Hom.: 22904 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.505 AC: 76614 AN: 151638 Hom.: 22910 Cov.: 32 AF XY: 0.494 AC XY: 36586 AN XY: 74078

African (AFR) AF: 0.264 AC: 10920 AN: 41432

American (AMR) AF: 0.409 AC: 6210 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2028 AN: 3464

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5178

South Asian (SAS) AF: 0.253 AC: 1219 AN: 4814

European-Finnish (FIN) AF: 0.694 AC: 7339 AN: 10580

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 46920 AN: 67664

Other (OTH) AF: 0.519 AC: 1093 AN: 2106

Alfa AF: 0.611 Hom.: 120253

Bravo AF: 0.475

Asia WGS AF: 0.160 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.39
PhyloP100		-1.6

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: rs1408799;

hg19: chr9-12672097;

COSMIC: COSV60331987;