rs6080539

chr20-17048849-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.347

Alfa AF: 0.366 Hom.: 10119

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6080539; hg19: chr20-17029494;