rs8089099

Variant names:

• chr18-10078074-G-A
• rs8089099

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 0.226 in 152,148 control chromosomes in the GnomAD database, including 4,112 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 0.23 (4112 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 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: 0.226 AC: 34334 AN: 152030 Hom.: 4113 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.226 AC: 34344 AN: 152148 Hom.: 4112 Cov.: 33 AF XY: 0.225 AC XY: 16719 AN XY: 74384

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.235

Alfa AF: 0.259 Hom.: 5659

Bravo AF: 0.225

Asia WGS AF: 0.223 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8089099; hg19: chr18-10078071;