chr3-33223422-C-T

Variant names:

• chr3-33223422-C-T
• rs10222597

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 0.124 in 152,062 control chromosomes in the GnomAD database, including 1,930 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 0.12 (1930 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.124 AC: 18851 AN: 151944 Hom.: 1914 Cov.: 31

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.124 AC: 18888 AN: 152062 Hom.: 1930 Cov.: 31 AF XY: 0.135 AC XY: 10032 AN XY: 74292

African (AFR) AF: 0.0680 AC: 2821 AN: 41500

American (AMR) AF: 0.289 AC: 4418 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1673 AN: 5160

South Asian (SAS) AF: 0.224 AC: 1078 AN: 4810

European-Finnish (FIN) AF: 0.226 AC: 2385 AN: 10540

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0860 AC: 5847 AN: 67998

Other (OTH) AF: 0.139 AC: 294 AN: 2110

Alfa AF: 0.100 Hom.: 4583

Bravo AF: 0.128

Asia WGS AF: 0.330 AC: 1146 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	0.30
DANN	Benign	0.40
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10222597; hg19: chr3-33264914;