6-33160600-G-A

Variant names:

• chr6-33160600-G-A
• rs9368757

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 0.192 in 151,824 control chromosomes in the GnomAD database, including 3,309 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 0.19 (3309 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29108 AN: 151706 Hom.: 3295 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.192 AC: 29147 AN: 151824 Hom.: 3309 Cov.: 31 AF XY: 0.196 AC XY: 14573 AN XY: 74184

African (AFR) AF: 0.152 AC: 6311 AN: 41402

American (AMR) AF: 0.304 AC: 4641 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3464

East Asian (EAS) AF: 0.479 AC: 2474 AN: 5168

South Asian (SAS) AF: 0.165 AC: 792 AN: 4802

European-Finnish (FIN) AF: 0.226 AC: 2374 AN: 10482

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.171 AC: 11615 AN: 67930

Other (OTH) AF: 0.204 AC: 430 AN: 2106

Alfa AF: 0.180 Hom.: 3288

Bravo AF: 0.202

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.54
DANN	Benign	0.70
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs9368757; hg19: chr6-33128377; COSMIC: COSV59502195;