rs2296370

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr19-54713283-A-C
• chr19-54713283-A-G
• chr19-54713283-A-T

Variant summary

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

The ENST00000413439.5(LILRP2):​n.1957A>C 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: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: 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=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LILRP2	NR_003061.2	n.1957A>C		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.1957A>C		non_coding_transcript_exon_variant	Exon 7 of 7	1
LILRP2	ENST00000413572.1	n.*51A>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 396580 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 215022

African (AFR) AF: 0.00 AC: 0 AN: 10522

American (AMR) AF: 0.00 AC: 0 AN: 21906

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11972

East Asian (EAS) AF: 0.00 AC: 0 AN: 23182

South Asian (SAS) AF: 0.00 AC: 0 AN: 41508

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36170

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3128

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 226372

Other (OTH) AF: 0.00 AC: 0 AN: 21820

GnomAD4 genome Cov.: 28

Alfa AF: 0.00 Hom.: 75054

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.1
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;