20-59292423-G-A

Variant names:

• chr20-59292423-G-A
• rs6128532

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 0.514 in 152,030 control chromosomes in the GnomAD database, including 20,588 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 0.51 (20588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.514 AC: 78031 AN: 151912 Hom.: 20577 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.514 AC: 78085 AN: 152030 Hom.: 20588 Cov.: 32 AF XY: 0.522 AC XY: 38824 AN XY: 74314

African (AFR) AF: 0.484 AC: 20064 AN: 41452

American (AMR) AF: 0.557 AC: 8515 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1838 AN: 3466

East Asian (EAS) AF: 0.879 AC: 4547 AN: 5170

South Asian (SAS) AF: 0.717 AC: 3451 AN: 4816

European-Finnish (FIN) AF: 0.524 AC: 5544 AN: 10572

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32437 AN: 67956

Other (OTH) AF: 0.527 AC: 1112 AN: 2110

Alfa AF: 0.494 Hom.: 16099

Bravo AF: 0.512

Asia WGS AF: 0.777 AC: 2699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.67
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs6128532; hg19: chr20-57867478;