6-32658495-C-A

Variant names:

• chr6-32658495-C-A
• rs9273363

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 0.233 in 151,798 control chromosomes in the GnomAD database, including 4,679 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 0.23 (4679 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943
• Publications: 109 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35283 AN: 151680 Hom.: 4674 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.233 AC: 35315 AN: 151798 Hom.: 4679 Cov.: 31 AF XY: 0.234 AC XY: 17334 AN XY: 74170

African (AFR) AF: 0.122 AC: 5059 AN: 41434

American (AMR) AF: 0.283 AC: 4318 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 857 AN: 3456

East Asian (EAS) AF: 0.360 AC: 1852 AN: 5142

South Asian (SAS) AF: 0.253 AC: 1212 AN: 4788

European-Finnish (FIN) AF: 0.257 AC: 2711 AN: 10542

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18445 AN: 67846

Other (OTH) AF: 0.216 AC: 457 AN: 2112

Alfa AF: 0.262 Hom.: 17623

Bravo AF: 0.232

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.074
DANN	Benign	0.64
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs9273363; hg19: chr6-32626272;