19-54713283-A-G

Variant names:

• chr19-54713283-A-G
• rs2296370
• ENST00000413439.5:n.1957A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413439.5(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 ENST00000413439.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831
• Publications: 10 publications found

Genes affected

LILRP2 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413439.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRP2	NR_003061.2		n.1957A>G		non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRP2	ENST00000413439.5	TSL:1	n.1957A>G		non_coding_transcript_exon	Exon 7 of 7
	LILRP2	ENST00000413572.1	TSL:6	n.*51A>G		downstream_gene	N/A

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

African (AFR) AF: 0.668 AC: 6997 AN: 10472

American (AMR) AF: 0.589 AC: 12842 AN: 21794

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 6416 AN: 11926

East Asian (EAS) AF: 0.811 AC: 18747 AN: 23118

South Asian (SAS) AF: 0.556 AC: 22970 AN: 41314

European-Finnish (FIN) AF: 0.637 AC: 22980 AN: 36070

Middle Eastern (MID) AF: 0.546 AC: 1701 AN: 3116

European-Non Finnish (NFE) AF: 0.614 AC: 138434 AN: 225464

Other (OTH) AF: 0.616 AC: 13393 AN: 21748

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

African (AFR) AF: 0.662 AC: 27286 AN: 41218

American (AMR) AF: 0.601 AC: 9112 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1814 AN: 3466

East Asian (EAS) AF: 0.805 AC: 4139 AN: 5144

South Asian (SAS) AF: 0.590 AC: 2813 AN: 4768

European-Finnish (FIN) AF: 0.643 AC: 6760 AN: 10510

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 41971 AN: 67760

Other (OTH) AF: 0.622 AC: 1311 AN: 2108

Alfa AF: 0.619 Hom.: 75054

Bravo AF: 0.633

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.4
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs2296370; hg19: chr19-55224785;