18-22426997-C-G

Position:

• chr18-22426997-C-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 0.438 in 151,988 control chromosomes in the GnomAD database, including 15,702 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 0.44 (15702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66485 AN: 151872 Hom.: 15697 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.438 AC: 66517 AN: 151988 Hom.: 15702 Cov.: 32 AF XY: 0.438 AC XY: 32530 AN XY: 74260

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.417

Alfa AF: 0.361 Hom.: 1076

Bravo AF: 0.431

Asia WGS AF: 0.382 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs948384; hg19: chr18-20006960;