20-48466300-G-T

Variant names:

• chr20-48466300-G-T
• rs6019212

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 0.572 in 152,062 control chromosomes in the GnomAD database, including 25,857 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 0.57 (25857 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 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: 0.572 AC: 86866 AN: 151944 Hom.: 25798 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.572 AC: 86982 AN: 152062 Hom.: 25857 Cov.: 33 AF XY: 0.576 AC XY: 42803 AN XY: 74310

African (AFR) AF: 0.699 AC: 28975 AN: 41472

American (AMR) AF: 0.652 AC: 9961 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1567 AN: 3468

East Asian (EAS) AF: 0.765 AC: 3963 AN: 5180

South Asian (SAS) AF: 0.611 AC: 2948 AN: 4824

European-Finnish (FIN) AF: 0.457 AC: 4823 AN: 10550

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32884 AN: 67968

Other (OTH) AF: 0.549 AC: 1159 AN: 2112

Alfa AF: 0.517 Hom.: 4247

Bravo AF: 0.594

Asia WGS AF: 0.636 AC: 2211 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	5.6
DANN	Benign	0.61
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6019212; hg19: chr20-47094546;