rs2858333

chr6-32713308-A-Gchr6-32713308-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;