9-12659691-G-A

Variant names:

• chr9-12659691-G-A
• rs4741242
• ENST00000803542.1:n.310-28084C>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.310-28084C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,224 control chromosomes in the GnomAD database, including 64,372 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 0.92 (64372 hom., cov: 32)
• Consequence: LURAP1L-AS1 ENST00000803542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 1 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803542.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LURAP1L-AS1	ENST00000803542.1		n.310-28084C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139704 AN: 152108 Hom.: 64314 Cov.: 32

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.919 AC: 139821 AN: 152224 Hom.: 64372 Cov.: 32 AF XY: 0.912 AC XY: 67904 AN XY: 74420

African (AFR) AF: 0.973 AC: 40401 AN: 41536

American (AMR) AF: 0.899 AC: 13749 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3051 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4176 AN: 5142

South Asian (SAS) AF: 0.764 AC: 3679 AN: 4818

European-Finnish (FIN) AF: 0.900 AC: 9551 AN: 10610

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62159 AN: 68030

Other (OTH) AF: 0.920 AC: 1943 AN: 2112

Alfa AF: 0.921 Hom.: 10503

Bravo AF: 0.925

Asia WGS AF: 0.781 AC: 2718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.34
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs4741242; hg19: chr9-12659691;