20-17788683-G-T

Position:

• chr20-17788683-G-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 0.386 in 152,054 control chromosomes in the GnomAD database, including 11,995 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 0.39 (11995 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918

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 (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58717 AN: 151938 Hom.: 11990 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.386 AC: 58759 AN: 152054 Hom.: 11995 Cov.: 32 AF XY: 0.391 AC XY: 29080 AN XY: 74342

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.373

Alfa AF: 0.416 Hom.: 12818

Bravo AF: 0.369

Asia WGS AF: 0.369 AC: 1282 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	0.55
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6080826; hg19: chr20-17769328;