20-17059314-C-T

Variant names:

• chr20-17059314-C-T
• rs6080544

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 0.344 in 152,142 control chromosomes in the GnomAD database, including 11,136 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 0.34 (11136 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52303 AN: 152022 Hom.: 11128 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.344 AC: 52330 AN: 152142 Hom.: 11136 Cov.: 32 AF XY: 0.354 AC XY: 26292 AN XY: 74368

African (AFR) AF: 0.107 AC: 4432 AN: 41524

American (AMR) AF: 0.470 AC: 7187 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1446 AN: 3470

East Asian (EAS) AF: 0.749 AC: 3870 AN: 5166

South Asian (SAS) AF: 0.515 AC: 2486 AN: 4826

European-Finnish (FIN) AF: 0.464 AC: 4905 AN: 10578

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26906 AN: 67972

Other (OTH) AF: 0.371 AC: 782 AN: 2108

Alfa AF: 0.385 Hom.: 52772

Bravo AF: 0.335

Asia WGS AF: 0.610 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.54
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6080544; hg19: chr20-17039959;