rs1420106

Positions:

• chr2-102418584-A-G

Variant summary

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

The 2-102418584-A-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,102 control chromosomes in the GnomAD database, including 46,600 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 0.77 (46599 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: IL18RAP NM_001393486.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

Genes affected

IL18RAP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL18RAP	NM_001393486.1			upstream_gene_variant
IL18RAP	NM_001393489.1			upstream_gene_variant
IL18RAP	XM_024453197.2			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117664 AN: 151980 Hom.: 46551 Cov.: 32

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.759

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 FIN exome AF: 1.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.774 AC: 117763 AN: 152098 Hom.: 46599 Cov.: 32 AF XY: 0.768 AC XY: 57087 AN XY: 74326

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.761

Alfa AF: 0.755 Hom.: 42704

Bravo AF: 0.764

Asia WGS AF: 0.583 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	10
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1420106; hg19: chr2-103035044;