18-23033307-G-A

Position:

• chr18-23033307-G-A

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 0.492 in 152,056 control chromosomes in the GnomAD database, including 21,696 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 0.49 (21696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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: 0.492 AC: 74750 AN: 151938 Hom.: 21698 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.492 AC: 74749 AN: 152056 Hom.: 21696 Cov.: 32 AF XY: 0.494 AC XY: 36719 AN XY: 74338

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.557

Alfa AF: 0.601 Hom.: 13078

Bravo AF: 0.469

Asia WGS AF: 0.489 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9954649; hg19: chr18-20613270;