rs10491744

Variant names:

• chr9-12720107-A-G
• rs10491744
• ENST00000417638.1:n.273-19481T>C

Variant summary

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

The ENST00000417638.1(LURAP1L-AS1):​n.273-19481T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,876 control chromosomes in the GnomAD database, including 18,090 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 (18090 hom., cov: 33)
• Consequence: LURAP1L-AS1 ENST00000417638.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417638.1. 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
	LURAP1L-AS1	NR_125775.1		n.317-19481T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LURAP1L-AS1	ENST00000417638.1	TSL:3	n.273-19481T>C		intron	N/A
	LURAP1L-AS1	ENST00000650458.1		n.193-20752T>C		intron	N/A
	LURAP1L-AS1	ENST00000654076.1		n.159-19481T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65464 AN: 151758 Hom.: 18087 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.0201

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.431 AC: 65474 AN: 151876 Hom.: 18090 Cov.: 33 AF XY: 0.423 AC XY: 31431 AN XY: 74248

African (AFR) AF: 0.136 AC: 5617 AN: 41342

American (AMR) AF: 0.403 AC: 6154 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1669 AN: 3468

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5174

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4818

European-Finnish (FIN) AF: 0.640 AC: 6764 AN: 10562

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42548 AN: 67944

Other (OTH) AF: 0.442 AC: 931 AN: 2106

Alfa AF: 0.540 Hom.: 4643

Bravo AF: 0.403

Asia WGS AF: 0.137 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.73
DANN	Benign	0.70
PhyloP100		-0.92

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: rs10491744;

hg19: chr9-12720106;