18-22208340-T-G

Variant names:

• chr18-22208340-T-G
• rs1426022

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.631 AC: 26152 AN: 41462

American (AMR) AF: 0.598 AC: 9137 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1792 AN: 3470

East Asian (EAS) AF: 0.447 AC: 2310 AN: 5164

South Asian (SAS) AF: 0.538 AC: 2590 AN: 4816

European-Finnish (FIN) AF: 0.501 AC: 5290 AN: 10552

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36652 AN: 67966

Other (OTH) AF: 0.553 AC: 1169 AN: 2114

Alfa AF: 0.545 Hom.: 69584

Bravo AF: 0.577

Asia WGS AF: 0.480 AC: 1670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.48
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1426022; hg19: chr18-19788303;