20-57560143-C-T

Variant names:

• chr20-57560143-C-T
• rs1328757

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 0.41 in 152,088 control chromosomes in the GnomAD database, including 13,147 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 0.41 (13147 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62393 AN: 151970 Hom.: 13153 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.410 AC: 62387 AN: 152088 Hom.: 13147 Cov.: 33 AF XY: 0.408 AC XY: 30348 AN XY: 74348

African (AFR) AF: 0.330 AC: 13691 AN: 41482

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

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1540 AN: 3468

East Asian (EAS) AF: 0.368 AC: 1906 AN: 5178

South Asian (SAS) AF: 0.427 AC: 2062 AN: 4826

European-Finnish (FIN) AF: 0.457 AC: 4832 AN: 10576

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31000 AN: 67954

Other (OTH) AF: 0.431 AC: 911 AN: 2114

Alfa AF: 0.439 Hom.: 39873

Bravo AF: 0.402

Asia WGS AF: 0.382 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1328757; hg19: chr20-56135199;