20-57853649-T-G

Variant names:

• chr20-57853649-T-G
• rs12481680

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 0.128 in 152,230 control chromosomes in the GnomAD database, including 1,386 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 (1386 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 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: 0.128 AC: 19436 AN: 152112 Hom.: 1383 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.128 AC: 19455 AN: 152230 Hom.: 1386 Cov.: 33 AF XY: 0.134 AC XY: 9989 AN XY: 74424

African (AFR) AF: 0.125 AC: 5173 AN: 41526

American (AMR) AF: 0.166 AC: 2538 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1720 AN: 5166

South Asian (SAS) AF: 0.183 AC: 881 AN: 4826

European-Finnish (FIN) AF: 0.129 AC: 1369 AN: 10604

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7072 AN: 68020

Other (OTH) AF: 0.122 AC: 258 AN: 2114

Alfa AF: 0.116 Hom.: 2276

Bravo AF: 0.129

Asia WGS AF: 0.260 AC: 901 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.9
DANN	Benign	0.88
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs12481680; hg19: chr20-56428705;