19-54713465-T-C

Variant names:

• chr19-54713465-T-C
• rs10423751
• ENST00000413439.5:n.*12T>C

Variant summary

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

The ENST00000413439.5(LILRP2):​n.*12T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 197,692 control chromosomes in the GnomAD database, including 28,033 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 0.52 (20906 hom., cov: 28)
  • Exomes 𝑓: 0.55 (7127 hom.)
• Consequence: LILRP2 ENST00000413439.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.41
• 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 (Cadd=0.404).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 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.*13T>C		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LILRP2	ENST00000413439.5	TSL:1	n.*12T>C		downstream_gene	N/A
	LILRP2	ENST00000413572.1	TSL:6	n.*233T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.521 AC: 78873 AN: 151330 Hom.: 20894 Cov.: 28

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.520

GnomAD4 exome AF: 0.549 AC: 25374 AN: 46244 Hom.: 7127 Cov.: 0 AF XY: 0.550 AC XY: 13396 AN XY: 24342

African (AFR) AF: 0.458 AC: 553 AN: 1208

American (AMR) AF: 0.459 AC: 1074 AN: 2338

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 622 AN: 1264

East Asian (EAS) AF: 0.312 AC: 485 AN: 1556

South Asian (SAS) AF: 0.558 AC: 3028 AN: 5430

European-Finnish (FIN) AF: 0.529 AC: 1081 AN: 2042

Middle Eastern (MID) AF: 0.568 AC: 125 AN: 220

European-Non Finnish (NFE) AF: 0.575 AC: 16810 AN: 29210

Other (OTH) AF: 0.536 AC: 1596 AN: 2976

GnomAD4 genome AF: 0.521 AC: 78925 AN: 151448 Hom.: 20906 Cov.: 28 AF XY: 0.515 AC XY: 38108 AN XY: 73968

African (AFR) AF: 0.459 AC: 18949 AN: 41314

American (AMR) AF: 0.480 AC: 7286 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1614 AN: 3466

East Asian (EAS) AF: 0.331 AC: 1697 AN: 5128

South Asian (SAS) AF: 0.587 AC: 2809 AN: 4788

European-Finnish (FIN) AF: 0.518 AC: 5438 AN: 10488

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39452 AN: 67788

Other (OTH) AF: 0.522 AC: 1094 AN: 2094

Alfa AF: 0.553 Hom.: 73893

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.40
PhyloP100		-3.4

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: rs10423751;