rs12033699

Variant names:

• chr1-226467310-A-G
• rs12033699

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 0.269 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.269 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

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.264

Alfa AF: 0.232 Hom.: 8799

Bravo AF: 0.266

Asia WGS AF: 0.367 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12033699; hg19: chr1-226655011;