chr20-45173856-A-G

Variant names:

• chr20-45173856-A-G
• rs55767422

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 0.152 in 151,866 control chromosomes in the GnomAD database, including 1,862 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 0.15 (1862 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23040 AN: 151748 Hom.: 1857 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.152 AC: 23079 AN: 151866 Hom.: 1862 Cov.: 31 AF XY: 0.153 AC XY: 11329 AN XY: 74212

African (AFR) AF: 0.122 AC: 5049 AN: 41416

American (AMR) AF: 0.130 AC: 1980 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 719 AN: 3464

East Asian (EAS) AF: 0.0347 AC: 180 AN: 5190

South Asian (SAS) AF: 0.144 AC: 691 AN: 4798

European-Finnish (FIN) AF: 0.188 AC: 1982 AN: 10528

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11775 AN: 67896

Other (OTH) AF: 0.167 AC: 353 AN: 2110

Alfa AF: 0.163 Hom.: 262

Bravo AF: 0.146

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs55767422; hg19: chr20-43802497;