20-16780960-G-T

Position:

• chr20-16780960-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 0.28 in 152,076 control chromosomes in the GnomAD database, including 6,682 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 0.28 (6682 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 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: 0.280 AC: 42608 AN: 151958 Hom.: 6679 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.280 AC: 42618 AN: 152076 Hom.: 6682 Cov.: 33 AF XY: 0.282 AC XY: 20928 AN XY: 74332

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.271

Alfa AF: 0.319 Hom.: 1862

Bravo AF: 0.265

Asia WGS AF: 0.198 AC: 689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.59
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4813250; hg19: chr20-16761605;