20-54935451-G-A

Variant names:

• chr20-54935451-G-A
• rs415667

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 0.31 in 151,706 control chromosomes in the GnomAD database, including 7,441 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 0.31 (7441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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: 0.310 AC: 47013 AN: 151590 Hom.: 7426 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.310 AC: 47061 AN: 151706 Hom.: 7441 Cov.: 32 AF XY: 0.301 AC XY: 22328 AN XY: 74110

African (AFR) AF: 0.321 AC: 13271 AN: 41338

American (AMR) AF: 0.304 AC: 4631 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 951 AN: 3464

East Asian (EAS) AF: 0.0852 AC: 440 AN: 5162

South Asian (SAS) AF: 0.166 AC: 797 AN: 4810

European-Finnish (FIN) AF: 0.252 AC: 2635 AN: 10476

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23124 AN: 67902

Other (OTH) AF: 0.315 AC: 660 AN: 2098

Alfa AF: 0.326 Hom.: 1008

Bravo AF: 0.314

Asia WGS AF: 0.131 AC: 456 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.53
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs415667; hg19: chr20-53551990;