chr20-45918429-A-G

Variant names:

• chr20-45918429-A-G
• rs17447545

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 0.197 in 121,010 control chromosomes in the GnomAD database, including 2,320 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 0.20 (2320 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.226 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: 0.197 AC: 23770 AN: 120908 Hom.: 2314 Cov.: 30

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.197 AC: 23798 AN: 121010 Hom.: 2320 Cov.: 30 AF XY: 0.194 AC XY: 11589 AN XY: 59756

African (AFR) AF: 0.224 AC: 6967 AN: 31160

American (AMR) AF: 0.147 AC: 1888 AN: 12876

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 551 AN: 2368

East Asian (EAS) AF: 0.0258 AC: 123 AN: 4762

South Asian (SAS) AF: 0.239 AC: 976 AN: 4092

European-Finnish (FIN) AF: 0.156 AC: 1364 AN: 8758

Middle Eastern (MID) AF: 0.168 AC: 39 AN: 232

European-Non Finnish (NFE) AF: 0.210 AC: 11408 AN: 54388

Other (OTH) AF: 0.197 AC: 318 AN: 1616

Alfa AF: 0.180 Hom.: 9574

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs17447545; hg19: chr20-44547068;