18-22596123-A-G

Variant names:

• chr18-22596123-A-G
• rs8087945

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;