chr20-3072850-G-C

Variant names:

• chr20-3072850-G-C
• rs2740209

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 0.27 in 152,184 control chromosomes in the GnomAD database, including 6,118 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 0.27 (6118 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41013 AN: 152066 Hom.: 6105 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.270 AC: 41049 AN: 152184 Hom.: 6118 Cov.: 33 AF XY: 0.269 AC XY: 20010 AN XY: 74380

African (AFR) AF: 0.151 AC: 6266 AN: 41556

American (AMR) AF: 0.378 AC: 5782 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1009 AN: 3472

East Asian (EAS) AF: 0.270 AC: 1391 AN: 5160

South Asian (SAS) AF: 0.271 AC: 1306 AN: 4826

European-Finnish (FIN) AF: 0.265 AC: 2803 AN: 10592

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21780 AN: 67974

Other (OTH) AF: 0.255 AC: 539 AN: 2112

Alfa AF: 0.177 Hom.: 394

Bravo AF: 0.276

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.67
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2740209; hg19: chr20-3053496;