rs10423751

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr19-54713465-T-A
• chr19-54713465-T-C
• chr19-54713465-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000413439.5(LILRP2):​n.*12T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00054 in 198,144 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00059 (0 hom., cov: 28)
  • Exomes 𝑓: 0.00039 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.311).

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>A		downstream_gene	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.000587 AC: 89 AN: 151586 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.000267

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000132

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00110

Gnomad OTH AF: 0.000481

GnomAD4 exome AF: 0.000388 AC: 18 AN: 46440 Hom.: 0 Cov.: 0 AF XY: 0.000450 AC XY: 11 AN XY: 24448

African (AFR) AF: 0.00 AC: 0 AN: 1214

American (AMR) AF: 0.00 AC: 0 AN: 2344

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1272

East Asian (EAS) AF: 0.00 AC: 0 AN: 1562

South Asian (SAS) AF: 0.00 AC: 0 AN: 5452

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2048

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 220

European-Non Finnish (NFE) AF: 0.000613 AC: 18 AN: 29340

Other (OTH) AF: 0.00 AC: 0 AN: 2988

GnomAD4 genome AF: 0.000587 AC: 89 AN: 151704 Hom.: 0 Cov.: 28 AF XY: 0.000513 AC XY: 38 AN XY: 74122

African (AFR) AF: 0.000266 AC: 11 AN: 41374

American (AMR) AF: 0.000131 AC: 2 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5128

South Asian (SAS) AF: 0.00 AC: 0 AN: 4800

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10516

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00110 AC: 75 AN: 67896

Other (OTH) AF: 0.000476 AC: 1 AN: 2100

Alfa AF: 0.00000210 Hom.: 73893

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.31
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;