chr8-116580190-G-A

Variant names:

• chr8-116580190-G-A
• rs6469650

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 0.608 in 151,988 control chromosomes in the GnomAD database, including 29,393 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 0.61 (29393 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92356 AN: 151870 Hom.: 29347 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.608 AC: 92463 AN: 151988 Hom.: 29393 Cov.: 31 AF XY: 0.612 AC XY: 45440 AN XY: 74276

African (AFR) AF: 0.785 AC: 32540 AN: 41468

American (AMR) AF: 0.590 AC: 9004 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1956 AN: 3468

East Asian (EAS) AF: 0.858 AC: 4425 AN: 5160

South Asian (SAS) AF: 0.619 AC: 2984 AN: 4818

European-Finnish (FIN) AF: 0.531 AC: 5606 AN: 10556

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34257 AN: 67952

Other (OTH) AF: 0.568 AC: 1198 AN: 2110

Alfa AF: 0.528 Hom.: 41942

Bravo AF: 0.617

Asia WGS AF: 0.723 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.16
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6469650; hg19: chr8-117592429;