rs12379024

chr9-12717406-G-A

Variant summary

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

The NR_125775.1(LURAP1L-AS1):n.317-16780C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,974 control chromosomes in the GnomAD database, including 18,046 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 (18046 hom., cov: 32)
• Consequence: LURAP1L-AS1 NR_125775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

Genes affected

LURAP1L-AS1 (HGNC:49761): (LURAP1L antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LURAP1L-AS1	NR_125775.1	n.317-16780C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LURAP1L-AS1	ENST00000417638.1	n.273-16780C>T		intron_variant, non_coding_transcript_variant		3
LURAP1L-AS1	ENST00000650458.1	n.193-18051C>T		intron_variant, non_coding_transcript_variant
LURAP1L-AS1	ENST00000654076.1	n.159-16780C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65373 AN: 151854 Hom.: 18044 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.430 AC: 65382 AN: 151974 Hom.: 18046 Cov.: 32 AF XY: 0.423 AC XY: 31398 AN XY: 74268

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.0198

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.440

Alfa AF: 0.531 Hom.: 5107

Bravo AF: 0.403

Asia WGS AF: 0.137 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.012
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12379024; hg19: chr9-12717405;