chr8-28760798-C-T

Variant names:

• chr8-28760798-C-T
• rs12544882

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0481 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

Gnomad4 AFR AF: 0.0340

Gnomad4 AMR AF: 0.0844

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.0282

Gnomad4 SAS AF: 0.0708

Gnomad4 FIN AF: 0.0422

Gnomad4 NFE AF: 0.0495

Gnomad4 OTH AF: 0.0506

Alfa AF: 0.0545 Hom.: 130

Bravo AF: 0.0491

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12544882; hg19: chr8-28618315;