rs2858884

Positions:

• chr6-32732306-A-C

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 0.231 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.0698

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.240

Alfa AF: 0.193 Hom.: 707

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858884; hg19: chr6-32700083;