rs6080826

Variant names:

• chr20-17788683-G-T
• rs6080826

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 0.386 in 152,054 control chromosomes in the GnomAD database, including 11,995 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 0.39 (11995 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 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: 0.386 AC: 58717 AN: 151938 Hom.: 11990 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.386 AC: 58759 AN: 152054 Hom.: 11995 Cov.: 32 AF XY: 0.391 AC XY: 29080 AN XY: 74342

African (AFR) AF: 0.274 AC: 11354 AN: 41466

American (AMR) AF: 0.394 AC: 6024 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1137 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1997 AN: 5168

South Asian (SAS) AF: 0.350 AC: 1685 AN: 4818

European-Finnish (FIN) AF: 0.566 AC: 5974 AN: 10562

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.433 AC: 29426 AN: 67976

Other (OTH) AF: 0.373 AC: 788 AN: 2110

Alfa AF: 0.404 Hom.: 25294

Bravo AF: 0.369

Asia WGS AF: 0.369 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.55
DANN	Benign	0.29
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs6080826; hg19: chr20-17769328;