rs333229

Variant names:

• chr2-108014928-G-T
• rs333229

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 0.268 in 151,860 control chromosomes in the GnomAD database, including 5,697 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 (5697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 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: 0.268 AC: 40626 AN: 151742 Hom.: 5690 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.268 AC: 40657 AN: 151860 Hom.: 5697 Cov.: 32 AF XY: 0.266 AC XY: 19725 AN XY: 74210

African (AFR) AF: 0.352 AC: 14574 AN: 41408

American (AMR) AF: 0.273 AC: 4166 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 744 AN: 3470

East Asian (EAS) AF: 0.135 AC: 694 AN: 5154

South Asian (SAS) AF: 0.216 AC: 1039 AN: 4814

European-Finnish (FIN) AF: 0.221 AC: 2331 AN: 10546

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16230 AN: 67918

Other (OTH) AF: 0.230 AC: 486 AN: 2110

Alfa AF: 0.252 Hom.: 1779

Bravo AF: 0.274

Asia WGS AF: 0.195 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.57
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs333229; hg19: chr2-108631384;