chr20-57109027-A-G

Variant names:

• chr20-57109027-A-G
• rs913068

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 0.238 in 152,190 control chromosomes in the GnomAD database, including 4,660 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 0.24 (4660 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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: 0.238 AC: 36177 AN: 152072 Hom.: 4664 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.238 AC: 36174 AN: 152190 Hom.: 4660 Cov.: 33 AF XY: 0.233 AC XY: 17368 AN XY: 74408

African (AFR) AF: 0.162 AC: 6723 AN: 41532

American (AMR) AF: 0.254 AC: 3879 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 851 AN: 3466

East Asian (EAS) AF: 0.393 AC: 2026 AN: 5150

South Asian (SAS) AF: 0.186 AC: 899 AN: 4824

European-Finnish (FIN) AF: 0.214 AC: 2265 AN: 10602

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18623 AN: 67998

Other (OTH) AF: 0.255 AC: 540 AN: 2114

Alfa AF: 0.261 Hom.: 16330

Bravo AF: 0.238

Asia WGS AF: 0.252 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs913068; hg19: chr20-55684083;