6-32732306-A-C

Variant names:

• chr6-32732306-A-C
• rs2858884

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 0.231 in 151,780 control chromosomes in the GnomAD database, including 4,306 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 (4306 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.231 AC: 34993 AN: 151660 Hom.: 4296 Cov.: 30

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0698

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.231 AC: 35025 AN: 151780 Hom.: 4306 Cov.: 30 AF XY: 0.226 AC XY: 16790 AN XY: 74174

African (AFR) AF: 0.307 AC: 12691 AN: 41380

American (AMR) AF: 0.194 AC: 2962 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3470

East Asian (EAS) AF: 0.0698 AC: 358 AN: 5132

South Asian (SAS) AF: 0.211 AC: 1008 AN: 4786

European-Finnish (FIN) AF: 0.189 AC: 1988 AN: 10522

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14386 AN: 67920

Other (OTH) AF: 0.240 AC: 507 AN: 2114

Alfa AF: 0.216 Hom.: 7006

Bravo AF: 0.229

Asia WGS AF: 0.165 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.66
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs2858884; hg19: chr6-32700083;