chr3-33223422-C-T

Position:

• chr3-33223422-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;