18-22208340-T-G

Variant names:

• chr18-22208340-T-G
• rs1426022

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;