6-32251066-A-G

Variant names:

• chr6-32251066-A-G
• rs3115573

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 0.415 in 152,032 control chromosomes in the GnomAD database, including 13,632 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 0.42 (13632 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 60 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63067 AN: 151914 Hom.: 13622 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.415 AC: 63100 AN: 152032 Hom.: 13632 Cov.: 32 AF XY: 0.414 AC XY: 30744 AN XY: 74322

African (AFR) AF: 0.343 AC: 14210 AN: 41456

American (AMR) AF: 0.513 AC: 7846 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2220 AN: 3464

East Asian (EAS) AF: 0.474 AC: 2451 AN: 5174

South Asian (SAS) AF: 0.576 AC: 2774 AN: 4814

European-Finnish (FIN) AF: 0.275 AC: 2907 AN: 10578

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29192 AN: 67946

Other (OTH) AF: 0.447 AC: 945 AN: 2112

Alfa AF: 0.439 Hom.: 49720

Bravo AF: 0.428

Asia WGS AF: 0.471 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs3115573; hg19: chr6-32218843;