20-17059314-C-T

Variant names:

• chr20-17059314-C-T
• rs6080544

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 0.344 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.344 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

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.371

Alfa AF: 0.394 Hom.: 25016

Bravo AF: 0.335

Asia WGS AF: 0.610 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6080544; hg19: chr20-17039959;