chr18-22596123-A-G

Variant names:

• chr18-22596123-A-G
• rs8087945

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 0.613 in 151,954 control chromosomes in the GnomAD database, including 29,086 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 0.61 (29086 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93186 AN: 151834 Hom.: 29080 Cov.: 31

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.613 AC: 93220 AN: 151954 Hom.: 29086 Cov.: 31 AF XY: 0.612 AC XY: 45437 AN XY: 74280

African (AFR) AF: 0.539 AC: 22286 AN: 41380

American (AMR) AF: 0.496 AC: 7568 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3472

East Asian (EAS) AF: 0.771 AC: 3995 AN: 5182

South Asian (SAS) AF: 0.645 AC: 3098 AN: 4804

European-Finnish (FIN) AF: 0.680 AC: 7183 AN: 10566

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44848 AN: 67966

Other (OTH) AF: 0.598 AC: 1263 AN: 2112

Alfa AF: 0.605 Hom.: 4570

Bravo AF: 0.597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.82
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs8087945; hg19: chr18-20176086;