12-28899977-G-A

Variant names:

• chr12-28899977-G-A
• rs753013

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 0.424 in 151,956 control chromosomes in the GnomAD database, including 14,487 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 0.42 (14487 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.569 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: 0.425 AC: 64479 AN: 151838 Hom.: 14477 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.424 AC: 64503 AN: 151956 Hom.: 14487 Cov.: 31 AF XY: 0.430 AC XY: 31962 AN XY: 74286

African (AFR) AF: 0.296 AC: 12259 AN: 41454

American (AMR) AF: 0.579 AC: 8838 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1645 AN: 3470

East Asian (EAS) AF: 0.341 AC: 1760 AN: 5160

South Asian (SAS) AF: 0.487 AC: 2349 AN: 4826

European-Finnish (FIN) AF: 0.510 AC: 5378 AN: 10540

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30891 AN: 67926

Other (OTH) AF: 0.418 AC: 882 AN: 2112

Alfa AF: 0.427 Hom.: 4128

Bravo AF: 0.424

Asia WGS AF: 0.415 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs753013; hg19: chr12-29052910;