rs2858333

Variant names:

• chr6-32713308-A-G
• rs2858333

Your query was ambiguous. Multiple possible variants found:

• chr6-32713308-A-G
• chr6-32713308-A-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 0.297 in 151,980 control chromosomes in the GnomAD database, including 7,156 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 0.30 (7156 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 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: 0.297 AC: 45090 AN: 151864 Hom.: 7158 Cov.: 31

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.297 AC: 45102 AN: 151980 Hom.: 7156 Cov.: 31 AF XY: 0.293 AC XY: 21751 AN XY: 74274

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.364

Alfa AF: 0.283 Hom.: 3530

Bravo AF: 0.311

Asia WGS AF: 0.456 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858333; hg19: chr6-32681085;