rs1121541

Variant names:

• chr9-12667049-C-T
• rs1121541
• ENST00000803542.1:n.310-35442G>A

Variant summary

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

The ENST00000803542.1(LURAP1L-AS1):​n.310-35442G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,936 control chromosomes in the GnomAD database, including 18,339 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 (18339 hom., cov: 31)
• Consequence: LURAP1L-AS1 ENST00000803542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 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.310-35442G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64964 AN: 151818 Hom.: 18343 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.428 AC: 64956 AN: 151936 Hom.: 18339 Cov.: 31 AF XY: 0.422 AC XY: 31369 AN XY: 74260

African (AFR) AF: 0.121 AC: 5023 AN: 41424

American (AMR) AF: 0.336 AC: 5119 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1676 AN: 3472

East Asian (EAS) AF: 0.0188 AC: 97 AN: 5160

South Asian (SAS) AF: 0.247 AC: 1189 AN: 4810

European-Finnish (FIN) AF: 0.687 AC: 7265 AN: 10572

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43110 AN: 67942

Other (OTH) AF: 0.431 AC: 907 AN: 2104

Alfa AF: 0.518 Hom.: 5413

Bravo AF: 0.387

Asia WGS AF: 0.138 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.46
DANN	Benign	0.71
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1121541; hg19: chr9-12667049;