8-107046808-A-T

Variant names:

• chr8-107046808-A-T
• rs2584365

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 0.264 in 152,006 control chromosomes in the GnomAD database, including 5,629 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 0.26 (5629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 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: 0.265 AC: 40176 AN: 151888 Hom.: 5625 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.264 AC: 40197 AN: 152006 Hom.: 5629 Cov.: 32 AF XY: 0.263 AC XY: 19567 AN XY: 74298

African (AFR) AF: 0.178 AC: 7368 AN: 41470

American (AMR) AF: 0.302 AC: 4606 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3466

East Asian (EAS) AF: 0.157 AC: 809 AN: 5164

South Asian (SAS) AF: 0.300 AC: 1447 AN: 4818

European-Finnish (FIN) AF: 0.282 AC: 2982 AN: 10576

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21338 AN: 67922

Other (OTH) AF: 0.272 AC: 576 AN: 2114

Alfa AF: 0.289 Hom.: 813

Bravo AF: 0.260

Asia WGS AF: 0.246 AC: 849 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	5.9
DANN	Benign	0.86
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2584365; hg19: chr8-108059036;