20-56126872-T-G

Variant names:

• chr20-56126872-T-G
• rs4811651

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.584 in 152,012 control chromosomes in the GnomAD database, including 31,134 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 0.58 (31134 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.755 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: 0.584 AC: 88697 AN: 151894 Hom.: 31130 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.584 AC: 88703 AN: 152012 Hom.: 31134 Cov.: 31 AF XY: 0.587 AC XY: 43641 AN XY: 74286

African (AFR) AF: 0.165 AC: 6858 AN: 41482

American (AMR) AF: 0.733 AC: 11190 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2824 AN: 3468

East Asian (EAS) AF: 0.572 AC: 2943 AN: 5142

South Asian (SAS) AF: 0.694 AC: 3337 AN: 4808

European-Finnish (FIN) AF: 0.709 AC: 7492 AN: 10572

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51709 AN: 67956

Other (OTH) AF: 0.663 AC: 1398 AN: 2110

Alfa AF: 0.548 Hom.: 2167

Bravo AF: 0.566

Asia WGS AF: 0.565 AC: 1964 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.68
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4811651; hg19: chr20-54701928;