20-33133887-G-A

Variant names:

• chr20-33133887-G-A
• rs6059104

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 0.397 in 152,084 control chromosomes in the GnomAD database, including 13,901 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 0.40 (13901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 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: 0.397 AC: 60267 AN: 151966 Hom.: 13873 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.397 AC: 60336 AN: 152084 Hom.: 13901 Cov.: 32 AF XY: 0.393 AC XY: 29211 AN XY: 74332

African (AFR) AF: 0.618 AC: 25636 AN: 41486

American (AMR) AF: 0.275 AC: 4204 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1643 AN: 3468

East Asian (EAS) AF: 0.0375 AC: 194 AN: 5178

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4822

European-Finnish (FIN) AF: 0.413 AC: 4361 AN: 10566

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21956 AN: 67968

Other (OTH) AF: 0.367 AC: 772 AN: 2104

Alfa AF: 0.317 Hom.: 5051

Bravo AF: 0.394

Asia WGS AF: 0.146 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		-0.065

Splicing

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

Other links and lift over

dbSNP: rs6059104; hg19: chr20-31721693;