19-54713283-A-G

Position:

• chr19-54713283-A-G

Variant summary

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

The NR_003061.2(LILRP2):​n.1957A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 546,372 control chromosomes in the GnomAD database, including 107,594 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 0.63 (30535 hom., cov: 28)
  • Exomes 𝑓: 0.62 (77059 hom.)
• Consequence: LILRP2 NR_003061.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LILRP2	NR_003061.2	n.1957A>G		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LILRP2	ENST00000413439.5	n.1957A>G		non_coding_transcript_exon_variant	7/7	1

Frequencies

GnomAD3 genomes AF: 0.634 AC: 95810 AN: 151232 Hom.: 30509 Cov.: 28

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.621

GnomAD4 exome AF: 0.619 AC: 244480 AN: 395022 Hom.: 77059 Cov.: 3 AF XY: 0.615 AC XY: 131695 AN XY: 214184

Gnomad4 AFR exome AF: 0.668

Gnomad4 AMR exome AF: 0.589

Gnomad4 ASJ exome AF: 0.538

Gnomad4 EAS exome AF: 0.811

Gnomad4 SAS exome AF: 0.556

Gnomad4 FIN exome AF: 0.637

Gnomad4 NFE exome AF: 0.614

Gnomad4 OTH exome AF: 0.616

GnomAD4 genome AF: 0.634 AC: 95887 AN: 151350 Hom.: 30535 Cov.: 28 AF XY: 0.632 AC XY: 46741 AN XY: 73948

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.622

Alfa AF: 0.612 Hom.: 35745

Bravo AF: 0.633

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2296370; hg19: chr19-55224785;