rs270779

chr19-54712758-G-Achr19-54712758-G-C

Variant summary

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

The NR_003061.2(LILRP2):n.1719-139G>A 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 0.527 in 218,992 control chromosomes in the GnomAD database, including 30,810 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 0.53 (21600 hom., cov: 30)
  • Exomes 𝑓: 0.52 (9210 hom.)
• Consequence: LILRP2 NR_003061.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357

Genes affected

LILRP2 (HGNC:15497): (leukocyte immunoglobulin-like receptor pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LILRP2	NR_003061.2	n.1719-139G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LILRP2	ENST00000413439.5	n.1719-139G>A		intron_variant, non_coding_transcript_variant		1
LILRP2	ENST00000413572.1	n.1196-139G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80770 AN: 151580 Hom.: 21589 Cov.: 30

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.531

GnomAD4 exome AF: 0.515 AC: 34669 AN: 67298 Hom.: 9210 AF XY: 0.511 AC XY: 18147 AN XY: 35526

Gnomad4 AFR exome AF: 0.540

Gnomad4 AMR exome AF: 0.484

Gnomad4 ASJ exome AF: 0.510

Gnomad4 EAS exome AF: 0.319

Gnomad4 SAS exome AF: 0.495

Gnomad4 FIN exome AF: 0.515

Gnomad4 NFE exome AF: 0.535

Gnomad4 OTH exome AF: 0.514

GnomAD4 genome AF: 0.533 AC: 80819 AN: 151694 Hom.: 21600 Cov.: 30 AF XY: 0.528 AC XY: 39136 AN XY: 74104

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.533

Alfa AF: 0.528 Hom.: 16455

Bravo AF: 0.529

Asia WGS AF: 0.469 AC: 1635 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	1.6
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs270779; hg19: chr19-55224260;