chr20-57896547-C-T

Variant names:

• chr20-57896547-C-T
• rs8124301

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 0.133 in 152,300 control chromosomes in the GnomAD database, including 1,698 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 0.13 (1698 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 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: 0.133 AC: 20179 AN: 152182 Hom.: 1678 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0936

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.133 AC: 20242 AN: 152300 Hom.: 1698 Cov.: 33 AF XY: 0.130 AC XY: 9653 AN XY: 74476

African (AFR) AF: 0.230 AC: 9552 AN: 41548

American (AMR) AF: 0.0933 AC: 1428 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3466

East Asian (EAS) AF: 0.0621 AC: 322 AN: 5182

South Asian (SAS) AF: 0.144 AC: 697 AN: 4824

European-Finnish (FIN) AF: 0.0606 AC: 643 AN: 10614

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0995 AC: 6766 AN: 68034

Other (OTH) AF: 0.143 AC: 302 AN: 2116

Alfa AF: 0.108 Hom.: 4297

Bravo AF: 0.138

Asia WGS AF: 0.159 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.75
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs8124301; hg19: chr20-56471603;