19-54713190-C-T

Variant names:

• chr19-54713190-C-T
• rs17207369
• ENST00000413439.5:n.1864C>T

Variant summary

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

The ENST00000413439.5(LILRP2):​n.1864C>T 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 0.77 in 863,326 control chromosomes in the GnomAD database, including 258,385 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 0.79 (47686 hom., cov: 27)
  • Exomes 𝑓: 0.77 (210699 hom.)
• Consequence: LILRP2 ENST00000413439.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LILRP2	NR_003061.2	n.1864C>T		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LILRP2	ENST00000413439.5	n.1864C>T		non_coding_transcript_exon_variant	Exon 7 of 7	1
LILRP2	ENST00000413572.1	n.1341C>T		non_coding_transcript_exon_variant	Exon 6 of 6	6

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119575 AN: 151526 Hom.: 47625 Cov.: 27

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.768

GnomAD4 exome AF: 0.766 AC: 545062 AN: 711682 Hom.: 210699 Cov.: 9 AF XY: 0.764 AC XY: 291116 AN XY: 381024

African (AFR) AF: 0.875 AC: 16819 AN: 19230

American (AMR) AF: 0.865 AC: 36681 AN: 42394

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 13374 AN: 20898

East Asian (EAS) AF: 0.986 AC: 35350 AN: 35852

South Asian (SAS) AF: 0.796 AC: 56517 AN: 71002

European-Finnish (FIN) AF: 0.742 AC: 37940 AN: 51118

Middle Eastern (MID) AF: 0.718 AC: 3074 AN: 4284

European-Non Finnish (NFE) AF: 0.738 AC: 318634 AN: 431842

Other (OTH) AF: 0.761 AC: 26673 AN: 35062

GnomAD4 genome AF: 0.789 AC: 119699 AN: 151644 Hom.: 47686 Cov.: 27 AF XY: 0.789 AC XY: 58471 AN XY: 74084

African (AFR) AF: 0.873 AC: 36106 AN: 41368

American (AMR) AF: 0.810 AC: 12312 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2168 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5095 AN: 5164

South Asian (SAS) AF: 0.813 AC: 3894 AN: 4788

European-Finnish (FIN) AF: 0.740 AC: 7773 AN: 10502

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49866 AN: 67850

Other (OTH) AF: 0.768 AC: 1612 AN: 2098

Alfa AF: 0.775 Hom.: 43008

Bravo AF: 0.798

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs17207369; hg19: chr19-55224692;