rs6080539

Variant names:

• chr20-17048849-T-C
• rs6080539

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 0.329 in 151,844 control chromosomes in the GnomAD database, including 9,317 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 0.33 (9317 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49864 AN: 151722 Hom.: 9309 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.329 AC: 49899 AN: 151844 Hom.: 9317 Cov.: 31 AF XY: 0.334 AC XY: 24805 AN XY: 74210

African (AFR) AF: 0.163 AC: 6768 AN: 41422

American (AMR) AF: 0.395 AC: 6017 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3382 AN: 5146

South Asian (SAS) AF: 0.491 AC: 2357 AN: 4796

European-Finnish (FIN) AF: 0.387 AC: 4078 AN: 10530

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24847 AN: 67924

Other (OTH) AF: 0.347 AC: 730 AN: 2104

Alfa AF: 0.357 Hom.: 12843

Bravo AF: 0.322

Asia WGS AF: 0.572 AC: 1985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.040
DANN	Benign	0.46
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6080539; hg19: chr20-17029494;