rs12544882

Positions:

• chr8-28760798-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;