19-54712758-G-A

Variant names:

• chr19-54712758-G-A
• rs270779
• ENST00000413439.5:n.1719-139G>A

Variant summary

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

The ENST00000413439.5(LILRP2):​n.1719-139G>A variant causes a intron 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 ENST00000413439.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357
• Publications: 7 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 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.1719-139G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRP2	ENST00000413439.5	TSL:1	n.1719-139G>A		intron	N/A
	LILRP2	ENST00000413572.1	TSL:6	n.1196-139G>A		intron	N/A

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

African (AFR) AF: 0.540 AC: 979 AN: 1812

American (AMR) AF: 0.484 AC: 1663 AN: 3436

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 850 AN: 1666

East Asian (EAS) AF: 0.319 AC: 831 AN: 2602

South Asian (SAS) AF: 0.495 AC: 4908 AN: 9910

European-Finnish (FIN) AF: 0.515 AC: 1947 AN: 3780

Middle Eastern (MID) AF: 0.494 AC: 155 AN: 314

European-Non Finnish (NFE) AF: 0.535 AC: 21278 AN: 39778

Other (OTH) AF: 0.514 AC: 2058 AN: 4000

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

African (AFR) AF: 0.548 AC: 22609 AN: 41292

American (AMR) AF: 0.508 AC: 7740 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1743 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1742 AN: 5166

South Asian (SAS) AF: 0.526 AC: 2529 AN: 4812

European-Finnish (FIN) AF: 0.510 AC: 5356 AN: 10492

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.550 AC: 37324 AN: 67922

Other (OTH) AF: 0.533 AC: 1121 AN: 2104

Alfa AF: 0.534 Hom.: 66179

Bravo AF: 0.529

Asia WGS AF: 0.469 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.26
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs270779; hg19: chr19-55224260;