8-28760798-C-T

Variant names:

• chr8-28760798-C-T
• rs12544882

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 0.0482 in 152,180 control chromosomes in the GnomAD database, including 198 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 0.048 (198 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0806 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: 0.0481 AC: 7321 AN: 152062 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0422

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0482 AC: 7333 AN: 152180 Hom.: 198 Cov.: 32 AF XY: 0.0488 AC XY: 3633 AN XY: 74386

African (AFR) AF: 0.0340 AC: 1413 AN: 41510

American (AMR) AF: 0.0844 AC: 1290 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 214 AN: 3466

East Asian (EAS) AF: 0.0282 AC: 146 AN: 5184

South Asian (SAS) AF: 0.0708 AC: 341 AN: 4818

European-Finnish (FIN) AF: 0.0422 AC: 447 AN: 10596

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0495 AC: 3363 AN: 68000

Other (OTH) AF: 0.0506 AC: 107 AN: 2114

Alfa AF: 0.0542 Hom.: 141

Bravo AF: 0.0491

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.60
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs12544882; hg19: chr8-28618315;