8-100829503-C-T

Variant names:

• chr8-100829503-C-T
• rs12680064

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 0.26 in 151,998 control chromosomes in the GnomAD database, including 5,707 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 (5707 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39544 AN: 151880 Hom.: 5700 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.260 AC: 39595 AN: 151998 Hom.: 5707 Cov.: 32 AF XY: 0.263 AC XY: 19498 AN XY: 74276

African (AFR) AF: 0.367 AC: 15208 AN: 41406

American (AMR) AF: 0.295 AC: 4510 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2075 AN: 5172

South Asian (SAS) AF: 0.263 AC: 1267 AN: 4810

European-Finnish (FIN) AF: 0.166 AC: 1749 AN: 10568

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13260 AN: 67988

Other (OTH) AF: 0.259 AC: 545 AN: 2108

Alfa AF: 0.219 Hom.: 12543

Bravo AF: 0.277

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12680064; hg19: chr8-101841731;