chr6-33017011-A-G

Variant names:

• chr6-33017011-A-G
• rs2116264

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 0.0976 in 152,306 control chromosomes in the GnomAD database, including 971 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 0.098 (971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 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: 0.0976 AC: 14855 AN: 152188 Hom.: 969 Cov.: 32

Gnomad AFR AF: 0.0219

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0828

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.0976 AC: 14859 AN: 152306 Hom.: 971 Cov.: 32 AF XY: 0.101 AC XY: 7514 AN XY: 74470

African (AFR) AF: 0.0219 AC: 910 AN: 41568

American (AMR) AF: 0.117 AC: 1783 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3472

East Asian (EAS) AF: 0.191 AC: 993 AN: 5186

South Asian (SAS) AF: 0.230 AC: 1108 AN: 4820

European-Finnish (FIN) AF: 0.0828 AC: 878 AN: 10604

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7931 AN: 68032

Other (OTH) AF: 0.126 AC: 266 AN: 2114

Alfa AF: 0.115 Hom.: 2039

Bravo AF: 0.0938

Asia WGS AF: 0.254 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	10
DANN	Benign	0.57
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2116264; hg19: chr6-32984788;