8-109208578-C-G

Variant names:

• chr8-109208578-C-G
• rs6469245

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 0.501 in 151,862 control chromosomes in the GnomAD database, including 20,522 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 0.50 (20522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 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: 0.501 AC: 75952 AN: 151744 Hom.: 20478 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.501 AC: 76055 AN: 151862 Hom.: 20522 Cov.: 32 AF XY: 0.504 AC XY: 37363 AN XY: 74198

African (AFR) AF: 0.697 AC: 28899 AN: 41442

American (AMR) AF: 0.512 AC: 7820 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 894 AN: 3470

East Asian (EAS) AF: 0.476 AC: 2447 AN: 5142

South Asian (SAS) AF: 0.531 AC: 2552 AN: 4810

European-Finnish (FIN) AF: 0.454 AC: 4779 AN: 10516

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.399 AC: 27116 AN: 67904

Other (OTH) AF: 0.451 AC: 951 AN: 2108

Alfa AF: 0.296 Hom.: 721

Bravo AF: 0.510

Asia WGS AF: 0.566 AC: 1948 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs6469245; hg19: chr8-110220807;