20-56254553-G-A

Variant names:

• chr20-56254553-G-A
• rs6099058

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 0.477 in 151,542 control chromosomes in the GnomAD database, including 18,548 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 0.48 (18548 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.477 AC: 72152 AN: 151420 Hom.: 18506 Cov.: 31

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.477 AC: 72255 AN: 151542 Hom.: 18548 Cov.: 31 AF XY: 0.477 AC XY: 35300 AN XY: 73994

African (AFR) AF: 0.685 AC: 28299 AN: 41312

American (AMR) AF: 0.401 AC: 6106 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1857 AN: 3464

East Asian (EAS) AF: 0.334 AC: 1713 AN: 5134

South Asian (SAS) AF: 0.468 AC: 2245 AN: 4798

European-Finnish (FIN) AF: 0.441 AC: 4604 AN: 10444

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26023 AN: 67856

Other (OTH) AF: 0.443 AC: 933 AN: 2106

Alfa AF: 0.413 Hom.: 61004

Bravo AF: 0.478

Asia WGS AF: 0.427 AC: 1486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.63
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs6099058; hg19: chr20-54829609;