20-57560878-C-G

Position:

• chr20-57560878-C-G

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 0.405 in 152,048 control chromosomes in the GnomAD database, including 12,904 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 0.41 (12904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.406 AC: 61618 AN: 151930 Hom.: 12911 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.405 AC: 61607 AN: 152048 Hom.: 12904 Cov.: 32 AF XY: 0.403 AC XY: 29969 AN XY: 74318

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.429

Alfa AF: 0.302 Hom.: 822

Bravo AF: 0.396

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.1
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: rs2071023; hg19: chr20-56135934;