19-54713190-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000413439.5(LILRP2):​n.1864C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 27)
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LILRP2	NR_003061.2	n.1864C>G		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>G		non_coding_transcript_exon_variant	Exon 7 of 7	1
LILRP2	ENST00000413572.1	n.1341C>G		non_coding_transcript_exon_variant	Exon 6 of 6	6

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome Cov.: 9

GnomAD4 genome Cov.: 27

Alfa AF: 0.00 Hom.: 43008

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
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;