rs10960752

Variant names:

• chr9-12675284-G-A
• rs10960752
• ENST00000803542.1:n.310-43677C>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.310-43677C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,818 control chromosomes in the GnomAD database, including 18,164 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 (18164 hom., cov: 32)
• Consequence: LURAP1L-AS1 ENST00000803542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 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.310-43677C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65720 AN: 151700 Hom.: 18164 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.433 AC: 65736 AN: 151818 Hom.: 18164 Cov.: 32 AF XY: 0.427 AC XY: 31662 AN XY: 74176

African (AFR) AF: 0.156 AC: 6468 AN: 41480

American (AMR) AF: 0.341 AC: 5183 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1628 AN: 3458

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5174

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4816

European-Finnish (FIN) AF: 0.682 AC: 7203 AN: 10558

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42663 AN: 67808

Other (OTH) AF: 0.433 AC: 912 AN: 2104

Alfa AF: 0.542 Hom.: 4790

Bravo AF: 0.396

Asia WGS AF: 0.131 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0080
DANN	Benign	0.58
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10960752; hg19: chr9-12675284;