rs12033699

Variant names:

• chr1-226467310-A-G
• rs12033699

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 0.269 in 151,982 control chromosomes in the GnomAD database, including 6,000 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 0.27 (6000 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40778 AN: 151864 Hom.: 5985 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.269 AC: 40827 AN: 151982 Hom.: 6000 Cov.: 31 AF XY: 0.268 AC XY: 19895 AN XY: 74314

African (AFR) AF: 0.375 AC: 15545 AN: 41400

American (AMR) AF: 0.182 AC: 2772 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 772 AN: 3466

East Asian (EAS) AF: 0.372 AC: 1927 AN: 5176

South Asian (SAS) AF: 0.319 AC: 1534 AN: 4810

European-Finnish (FIN) AF: 0.210 AC: 2222 AN: 10572

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15210 AN: 67984

Other (OTH) AF: 0.264 AC: 557 AN: 2110

Alfa AF: 0.239 Hom.: 15122

Bravo AF: 0.266

Asia WGS AF: 0.367 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.0
DANN	Benign	0.46
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs12033699; hg19: chr1-226655011;