19-54713465-T-C

Position:

• chr19-54713465-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.41

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54713465T>C		intergenic_region
LILRP2	NR_003061.2	n.*13T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LILRP2	ENST00000413439.5	n.*12T>C		downstream_gene_variant		1

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

Gnomad4 AFR exome AF: 0.458

Gnomad4 AMR exome AF: 0.459

Gnomad4 ASJ exome AF: 0.492

Gnomad4 EAS exome AF: 0.312

Gnomad4 SAS exome AF: 0.558

Gnomad4 FIN exome AF: 0.529

Gnomad4 NFE exome AF: 0.575

Gnomad4 OTH exome AF: 0.536

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

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.522

Alfa AF: 0.556 Hom.: 27239

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10423751; hg19: -;