rs10222597

Variant names:

• chr3-33223422-C-T
• rs10222597

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 0.124 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

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 (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

Gnomad4 AFR AF: 0.0680

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.0860

Gnomad4 OTH AF: 0.139

Alfa AF: 0.102 Hom.: 2386

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10222597; hg19: chr3-33264914;