rs1325127

Variant names:

• chr9-12668328-C-T
• rs1325127
• ENST00000803542.1:n.310-36721G>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.310-36721G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,042 control chromosomes in the GnomAD database, including 26,836 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 0.57 (26836 hom., cov: 33)
• Consequence: LURAP1L-AS1 ENST00000803542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 7 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 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.310-36721G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86966 AN: 151924 Hom.: 26825 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.572 AC: 87007 AN: 152042 Hom.: 26836 Cov.: 33 AF XY: 0.573 AC XY: 42578 AN XY: 74308

African (AFR) AF: 0.337 AC: 13953 AN: 41454

American (AMR) AF: 0.652 AC: 9946 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1959 AN: 3470

East Asian (EAS) AF: 0.719 AC: 3719 AN: 5174

South Asian (SAS) AF: 0.359 AC: 1731 AN: 4816

European-Finnish (FIN) AF: 0.754 AC: 7970 AN: 10568

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.675 AC: 45873 AN: 67990

Other (OTH) AF: 0.581 AC: 1224 AN: 2108

Alfa AF: 0.637 Hom.: 50770

Bravo AF: 0.561

Asia WGS AF: 0.551 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.43
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1325127; hg19: chr9-12668328;