12-114646254-A-G

Variant names:

• chr12-114646254-A-G
• rs61933115

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 0.718 in 151,678 control chromosomes in the GnomAD database, including 40,070 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 0.72 (40070 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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: 0.718 AC: 108839 AN: 151560 Hom.: 40021 Cov.: 30

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.718 AC: 108943 AN: 151678 Hom.: 40070 Cov.: 30 AF XY: 0.712 AC XY: 52790 AN XY: 74098

African (AFR) AF: 0.890 AC: 36860 AN: 41412

American (AMR) AF: 0.596 AC: 9092 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2238 AN: 3466

East Asian (EAS) AF: 0.792 AC: 4042 AN: 5106

South Asian (SAS) AF: 0.615 AC: 2950 AN: 4794

European-Finnish (FIN) AF: 0.644 AC: 6755 AN: 10484

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44783 AN: 67856

Other (OTH) AF: 0.670 AC: 1416 AN: 2112

Alfa AF: 0.678 Hom.: 4188

Bravo AF: 0.727

Asia WGS AF: 0.659 AC: 2293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.12
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs61933115; hg19: chr12-115084059;