chr6-32432567-C-A

Position:

• chr6-32432567-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 0.173 in 152,050 control chromosomes in the GnomAD database, including 2,859 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 0.17 (2859 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.172 AC: 26199 AN: 151932 Hom.: 2849 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.173 AC: 26239 AN: 152050 Hom.: 2859 Cov.: 32 AF XY: 0.170 AC XY: 12611 AN XY: 74326

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.178

Alfa AF: 0.122 Hom.: 2030

Bravo AF: 0.188

Asia WGS AF: 0.168 AC: 582 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9501626; hg19: chr6-32400344;