rs10960751

Variant names:

• chr9-12675264-T-C
• rs10960751
• ENST00000803542.1:n.310-43657A>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.310-43657A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,816 control chromosomes in the GnomAD database, including 18,218 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 0.44 (18218 hom., cov: 31)
• Consequence: LURAP1L-AS1 ENST00000803542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 6 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=-0.68).
• 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.310-43657A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66023 AN: 151698 Hom.: 18215 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.435 AC: 66048 AN: 151816 Hom.: 18218 Cov.: 31 AF XY: 0.429 AC XY: 31802 AN XY: 74178

African (AFR) AF: 0.163 AC: 6769 AN: 41512

American (AMR) AF: 0.342 AC: 5196 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1628 AN: 3462

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5176

South Asian (SAS) AF: 0.220 AC: 1059 AN: 4814

European-Finnish (FIN) AF: 0.681 AC: 7191 AN: 10552

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

European-Non Finnish (NFE) AF: 0.629 AC: 42655 AN: 67792

Other (OTH) AF: 0.436 AC: 917 AN: 2104

Alfa AF: 0.553 Hom.: 37219

Bravo AF: 0.398

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.1
DANN	Benign	0.42
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10960751; hg19: chr9-12675264;