18-22596123-A-G

Position:

• chr18-22596123-A-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 0.613 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22596123A>G		intergenic_region

Ensembl

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

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.598

Alfa AF: 0.609 Hom.: 4469

Bravo AF: 0.597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8087945; hg19: chr18-20176086;