6-32658495-C-A

Position:

• chr6-32658495-C-A

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 0.233 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.233 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

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.216

Alfa AF: 0.275 Hom.: 5266

Bravo AF: 0.232

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9273363; hg19: chr6-32626272;