rs8099654

Variant names:

• chr18-54997596-G-A
• rs8099654

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.317 in 152,122 control chromosomes in the GnomAD database, including 8,442 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 0.32 (8442 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 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: 0.317 AC: 48125 AN: 152004 Hom.: 8430 Cov.: 33

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.0911

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.317 AC: 48164 AN: 152122 Hom.: 8442 Cov.: 33 AF XY: 0.313 AC XY: 23294 AN XY: 74354

African (AFR) AF: 0.472 AC: 19582 AN: 41506

American (AMR) AF: 0.253 AC: 3866 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3468

East Asian (EAS) AF: 0.0917 AC: 475 AN: 5178

South Asian (SAS) AF: 0.356 AC: 1719 AN: 4828

European-Finnish (FIN) AF: 0.198 AC: 2097 AN: 10576

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18405 AN: 67970

Other (OTH) AF: 0.291 AC: 615 AN: 2110

Alfa AF: 0.290 Hom.: 1417

Bravo AF: 0.321

Asia WGS AF: 0.230 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.36
DANN	Benign	0.51
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs8099654; hg19: chr18-52664827;