rs1137134

Positions:

• chr9-12712157-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417638.1(LURAP1L-AS1):​n.273-11531C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,414 control chromosomes in the GnomAD database, including 16,501 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 0.41 (16501 hom., cov: 32)
• Consequence: LURAP1L-AS1 ENST00000417638.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

LURAP1L-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LURAP1L-AS1	NR_125775.1	n.317-11531C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LURAP1L-AS1	ENST00000417638.1	n.273-11531C>T		intron_variant		3
LURAP1L-AS1	ENST00000650458.1	n.193-12802C>T		intron_variant
LURAP1L-AS1	ENST00000654076.1	n.159-11531C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62193 AN: 151296 Hom.: 16502 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.411 AC: 62191 AN: 151414 Hom.: 16501 Cov.: 32 AF XY: 0.404 AC XY: 29903 AN XY: 73964

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.415

Alfa AF: 0.551 Hom.: 46403

Bravo AF: 0.383

Asia WGS AF: 0.133 AC: 463 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	1.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1137134; hg19: chr9-12712157;