chr6-32713308-A-G

Variant names:

• chr6-32713308-A-G
• rs2858333

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 0.297 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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.319 AC: 13225 AN: 41408

American (AMR) AF: 0.322 AC: 4920 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3470

East Asian (EAS) AF: 0.405 AC: 2093 AN: 5162

South Asian (SAS) AF: 0.456 AC: 2196 AN: 4812

European-Finnish (FIN) AF: 0.120 AC: 1273 AN: 10568

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18790 AN: 67962

Other (OTH) AF: 0.364 AC: 768 AN: 2110

Alfa AF: 0.290 Hom.: 5702

Bravo AF: 0.311

Asia WGS AF: 0.456 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.43
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2858333; hg19: chr6-32681085;