18-22208340-T-G

Position:

• chr18-22208340-T-G

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 0.564 in 152,028 control chromosomes in the GnomAD database, including 24,463 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 0.56 (24463 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22208340T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85619 AN: 151910 Hom.: 24427 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.556

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.564 AC: 85719 AN: 152028 Hom.: 24463 Cov.: 32 AF XY: 0.561 AC XY: 41717 AN XY: 74306

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.553

Alfa AF: 0.537 Hom.: 43274

Bravo AF: 0.577

Asia WGS AF: 0.480 AC: 1670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1426022; hg19: chr18-19788303;