rs12069733

Variant names:

• chr1-43475837-G-A
• rs12069733

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 0.371 in 151,800 control chromosomes in the GnomAD database, including 10,679 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 0.37 (10679 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.549 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: 0.371 AC: 56317 AN: 151682 Hom.: 10686 Cov.: 30

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.371 AC: 56336 AN: 151800 Hom.: 10679 Cov.: 30 AF XY: 0.374 AC XY: 27756 AN XY: 74172

African (AFR) AF: 0.344 AC: 14249 AN: 41402

American (AMR) AF: 0.376 AC: 5736 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1493 AN: 3466

East Asian (EAS) AF: 0.481 AC: 2475 AN: 5146

South Asian (SAS) AF: 0.566 AC: 2720 AN: 4802

European-Finnish (FIN) AF: 0.338 AC: 3557 AN: 10524

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24930 AN: 67910

Other (OTH) AF: 0.358 AC: 755 AN: 2108

Alfa AF: 0.380 Hom.: 6473

Bravo AF: 0.369

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.019
DANN	Benign	0.65
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs12069733; hg19: chr1-43941508;