6-32693166-A-G

Variant names:

• chr6-32693166-A-G
• rs9275245

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 0.536 in 151,738 control chromosomes in the GnomAD database, including 22,231 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 0.54 (22231 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 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: 0.536 AC: 81241 AN: 151620 Hom.: 22210 Cov.: 30

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.536 AC: 81318 AN: 151738 Hom.: 22231 Cov.: 30 AF XY: 0.540 AC XY: 40075 AN XY: 74158

African (AFR) AF: 0.524 AC: 21664 AN: 41382

American (AMR) AF: 0.634 AC: 9668 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2133 AN: 3468

East Asian (EAS) AF: 0.653 AC: 3376 AN: 5170

South Asian (SAS) AF: 0.416 AC: 1993 AN: 4796

European-Finnish (FIN) AF: 0.615 AC: 6452 AN: 10494

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34040 AN: 67866

Other (OTH) AF: 0.554 AC: 1167 AN: 2108

Alfa AF: 0.515 Hom.: 35819

Bravo AF: 0.543

Asia WGS AF: 0.595 AC: 2070 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.5
DANN	Benign	0.81
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs9275245; hg19: chr6-32660943; COSMIC: COSV70886663;