20-17059314-C-T

Position:

• chr20-17059314-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;