6-33055802-A-G

Variant names:

• chr6-33055802-A-G
• rs3130182

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 0.73 in 151,978 control chromosomes in the GnomAD database, including 40,886 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 0.73 (40886 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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: 0.730 AC: 110888 AN: 151860 Hom.: 40876 Cov.: 31

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.730 AC: 110942 AN: 151978 Hom.: 40886 Cov.: 31 AF XY: 0.738 AC XY: 54803 AN XY: 74298

African (AFR) AF: 0.706 AC: 29260 AN: 41422

American (AMR) AF: 0.649 AC: 9914 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3111 AN: 3470

East Asian (EAS) AF: 0.930 AC: 4813 AN: 5174

South Asian (SAS) AF: 0.836 AC: 4028 AN: 4816

European-Finnish (FIN) AF: 0.797 AC: 8429 AN: 10572

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49011 AN: 67944

Other (OTH) AF: 0.745 AC: 1572 AN: 2110

Alfa AF: 0.726 Hom.: 4765

Bravo AF: 0.714

Asia WGS AF: 0.849 AC: 2954 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	1.2
DANN	Benign	0.44
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs3130182; hg19: chr6-33023579;