chr6-132584048-C-A

Variant names:

• chr6-132584048-C-A
• rs9321354

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 0.212 in 152,064 control chromosomes in the GnomAD database, including 4,348 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 0.21 (4348 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 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: 0.212 AC: 32155 AN: 151946 Hom.: 4334 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.212 AC: 32202 AN: 152064 Hom.: 4348 Cov.: 32 AF XY: 0.216 AC XY: 16048 AN XY: 74336

African (AFR) AF: 0.350 AC: 14515 AN: 41448

American (AMR) AF: 0.252 AC: 3853 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3470

East Asian (EAS) AF: 0.326 AC: 1687 AN: 5174

South Asian (SAS) AF: 0.348 AC: 1677 AN: 4814

European-Finnish (FIN) AF: 0.0849 AC: 899 AN: 10584

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8133 AN: 67996

Other (OTH) AF: 0.246 AC: 520 AN: 2110

Alfa AF: 0.157 Hom.: 4322

Bravo AF: 0.226

Asia WGS AF: 0.366 AC: 1269 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.91
DANN	Benign	0.49
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9321354; hg19: chr6-132905187;