20-56265650-C-G

Variant names:

• chr20-56265650-C-G
• rs1980818

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 0.762 in 151,950 control chromosomes in the GnomAD database, including 44,302 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 0.76 (44302 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 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: 0.762 AC: 115732 AN: 151832 Hom.: 44280 Cov.: 30

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.762 AC: 115807 AN: 151950 Hom.: 44302 Cov.: 30 AF XY: 0.765 AC XY: 56809 AN XY: 74270

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.761

Alfa AF: 0.693 Hom.: 2083

Bravo AF: 0.764

Asia WGS AF: 0.824 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1980818; hg19: chr20-54840706;