rs60717610

Variant names:

• chr20-45173013-C-CATATA
• rs60717610

Your query was ambiguous. Multiple possible variants found:

• chr20-45173013-C-CATATA
• chr20-45173013-C-CATATG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.275 in 151,786 control chromosomes in the GnomAD database, including 6,889 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (6889 hom., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 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: 0.274 AC: 41601 AN: 151672 Hom.: 6863 Cov.: 21

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.275 AC: 41687 AN: 151786 Hom.: 6889 Cov.: 21 AF XY: 0.275 AC XY: 20392 AN XY: 74190

African (AFR) AF: 0.476 AC: 19648 AN: 41258

American (AMR) AF: 0.229 AC: 3503 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 806 AN: 3470

East Asian (EAS) AF: 0.103 AC: 535 AN: 5178

South Asian (SAS) AF: 0.164 AC: 790 AN: 4814

European-Finnish (FIN) AF: 0.232 AC: 2441 AN: 10530

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13019 AN: 67956

Other (OTH) AF: 0.274 AC: 578 AN: 2110

Alfa AF: 0.107 Hom.: 125

Asia WGS AF: 0.142 AC: 495 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs60717610; hg19: chr20-43801654;