20-32815620-A-G

Variant names:

• chr20-32815620-A-G
• rs242542

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 0.0694 in 152,174 control chromosomes in the GnomAD database, including 529 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 0.069 (529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.933
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.136 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: 0.0694 AC: 10560 AN: 152056 Hom.: 526 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0706

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0897

Gnomad OTH AF: 0.0659

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

GnomAD4 genome AF: 0.0694 AC: 10568 AN: 152174 Hom.: 529 Cov.: 32 AF XY: 0.0694 AC XY: 5167 AN XY: 74410

African (AFR) AF: 0.0182 AC: 755 AN: 41530

American (AMR) AF: 0.141 AC: 2153 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 263 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5186

South Asian (SAS) AF: 0.0706 AC: 340 AN: 4814

European-Finnish (FIN) AF: 0.0655 AC: 694 AN: 10596

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.0897 AC: 6096 AN: 67974

Other (OTH) AF: 0.0647 AC: 137 AN: 2116

Alfa AF: 0.0821 Hom.: 1029

Bravo AF: 0.0731

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs242542; hg19: chr20-31403426;