rs970946

chr9-12738691-C-Achr9-12738691-C-Gchr9-12738691-C-T

Variant summary

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

The NR_125775.1(LURAP1L-AS1):n.316+20861G>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 0.409 in 151,928 control chromosomes in the GnomAD database, including 14,224 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 (14224 hom., cov: 33)
• Consequence: LURAP1L-AS1 NR_125775.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LURAP1L-AS1	NR_125775.1	n.316+20861G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LURAP1L-AS1	ENST00000417638.1	n.272+20861G>T		intron_variant, non_coding_transcript_variant		3
LURAP1L-AS1	ENST00000650458.1	n.192+20861G>T		intron_variant, non_coding_transcript_variant
LURAP1L-AS1	ENST00000654076.1	n.158+20861G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62128 AN: 151808 Hom.: 14208 Cov.: 33

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.409 AC: 62190 AN: 151928 Hom.: 14224 Cov.: 33 AF XY: 0.415 AC XY: 30810 AN XY: 74260

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.421

Alfa AF: 0.336 Hom.: 18417

Bravo AF: 0.431

Asia WGS AF: 0.647 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.6
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs970946; hg19: chr9-12738690;