chr19-54713574-A-C

Variant names:

• chr19-54713574-A-C
• rs12982559
• ENST00000413439.5:n.*121A>C

Variant summary

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

The ENST00000413439.5(LILRP2):​n.*121A>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 158,124 control chromosomes in the GnomAD database, including 44,509 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 0.75 (42953 hom., cov: 31)
  • Exomes 𝑓: 0.71 (1556 hom.)
• Consequence: LILRP2 ENST00000413439.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRP2	NR_003061.2		n.*122A>C		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRP2	ENST00000413439.5	TSL:1	n.*121A>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113354 AN: 151900 Hom.: 42902 Cov.: 31

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.725

GnomAD4 exome AF: 0.709 AC: 4331 AN: 6106 Hom.: 1556 AF XY: 0.720 AC XY: 2279 AN XY: 3166

African (AFR) AF: 0.841 AC: 106 AN: 126

American (AMR) AF: 0.818 AC: 319 AN: 390

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 73 AN: 106

East Asian (EAS) AF: 0.983 AC: 171 AN: 174

South Asian (SAS) AF: 0.735 AC: 431 AN: 586

European-Finnish (FIN) AF: 0.674 AC: 116 AN: 172

Middle Eastern (MID) AF: 0.438 AC: 7 AN: 16

European-Non Finnish (NFE) AF: 0.685 AC: 2835 AN: 4138

Other (OTH) AF: 0.686 AC: 273 AN: 398

GnomAD4 genome AF: 0.746 AC: 113466 AN: 152018 Hom.: 42953 Cov.: 31 AF XY: 0.748 AC XY: 55570 AN XY: 74298

African (AFR) AF: 0.844 AC: 34998 AN: 41486

American (AMR) AF: 0.781 AC: 11945 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1996 AN: 3468

East Asian (EAS) AF: 0.986 AC: 5103 AN: 5176

South Asian (SAS) AF: 0.756 AC: 3631 AN: 4806

European-Finnish (FIN) AF: 0.704 AC: 7419 AN: 10542

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46059 AN: 67934

Other (OTH) AF: 0.726 AC: 1533 AN: 2112

Alfa AF: 0.702 Hom.: 120453

Bravo AF: 0.757

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12982559;

hg19: chr19-55225076;