rs388286

Variant names:

• chr20-56890368-C-T
• rs388286

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 0.45 in 151,996 control chromosomes in the GnomAD database, including 15,683 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 0.45 (15683 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.514 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: 0.450 AC: 68364 AN: 151880 Hom.: 15671 Cov.: 33

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.450 AC: 68406 AN: 151996 Hom.: 15683 Cov.: 33 AF XY: 0.458 AC XY: 33997 AN XY: 74298

African (AFR) AF: 0.389 AC: 16128 AN: 41464

American (AMR) AF: 0.470 AC: 7184 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1573 AN: 3470

East Asian (EAS) AF: 0.473 AC: 2436 AN: 5146

South Asian (SAS) AF: 0.531 AC: 2555 AN: 4814

European-Finnish (FIN) AF: 0.615 AC: 6511 AN: 10582

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30515 AN: 67920

Other (OTH) AF: 0.453 AC: 955 AN: 2110

Alfa AF: 0.453 Hom.: 10399

Bravo AF: 0.435

Asia WGS AF: 0.526 AC: 1831 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	1.5
DANN	Benign	0.54
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs388286; hg19: chr20-55465424;