chr18-9099202-G-A

Position:

• chr18-9099202-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 0.82 in 152,100 control chromosomes in the GnomAD database, including 51,221 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 0.82 (51221 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.843 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: 0.820 AC: 124586 AN: 151982 Hom.: 51177 Cov.: 30

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.820 AC: 124682 AN: 152100 Hom.: 51221 Cov.: 30 AF XY: 0.817 AC XY: 60707 AN XY: 74344

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.836

Alfa AF: 0.785 Hom.: 2371

Bravo AF: 0.818

Asia WGS AF: 0.755 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6506640; hg19: chr18-9099200;