rs6032006

Variant names:

• chr20-45126412-G-A
• rs6032006

Your query was ambiguous. Multiple possible variants found:

• chr20-45126412-G-A
• chr20-45126412-G-C

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 0.204 in 152,016 control chromosomes in the GnomAD database, including 3,547 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 0.20 (3547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 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: 0.203 AC: 30876 AN: 151898 Hom.: 3531 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.204 AC: 30941 AN: 152016 Hom.: 3547 Cov.: 32 AF XY: 0.202 AC XY: 15019 AN XY: 74284

African (AFR) AF: 0.304 AC: 12621 AN: 41454

American (AMR) AF: 0.149 AC: 2271 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3470

East Asian (EAS) AF: 0.0341 AC: 177 AN: 5184

South Asian (SAS) AF: 0.127 AC: 613 AN: 4826

European-Finnish (FIN) AF: 0.187 AC: 1971 AN: 10528

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11816 AN: 67972

Other (OTH) AF: 0.197 AC: 414 AN: 2104

Alfa AF: 0.111 Hom.: 174

Bravo AF: 0.205

Asia WGS AF: 0.0920 AC: 319 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	0.86
DANN	Benign	0.47
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs6032006; hg19: chr20-43755053; COSMIC: COSV65661401;