6-33510719-A-G

Variant names:

• chr6-33510719-A-G
• rs9296092

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 0.558 in 152,126 control chromosomes in the GnomAD database, including 26,849 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 0.56 (26849 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 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: 0.558 AC: 84884 AN: 152008 Hom.: 26848 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.558 AC: 84906 AN: 152126 Hom.: 26849 Cov.: 33 AF XY: 0.573 AC XY: 42585 AN XY: 74360

African (AFR) AF: 0.257 AC: 10661 AN: 41476

American (AMR) AF: 0.632 AC: 9661 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2246 AN: 3470

East Asian (EAS) AF: 0.941 AC: 4873 AN: 5176

South Asian (SAS) AF: 0.844 AC: 4072 AN: 4826

European-Finnish (FIN) AF: 0.758 AC: 8023 AN: 10586

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43397 AN: 67988

Other (OTH) AF: 0.587 AC: 1238 AN: 2110

Alfa AF: 0.627 Hom.: 80745

Bravo AF: 0.528

Asia WGS AF: 0.825 AC: 2868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.6
DANN	Benign	0.82
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs9296092; hg19: chr6-33478496;