rs6060239

Variant names:

• chr20-35106777-T-C
• rs6060239

Your query was ambiguous. Multiple possible variants found:

• chr20-35106777-T-C
• chr20-35106777-T-G

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 0.131 in 152,258 control chromosomes in the GnomAD database, including 1,365 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 (1365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19935 AN: 152138 Hom.: 1355 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0972

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.0768

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.131 AC: 19972 AN: 152258 Hom.: 1365 Cov.: 32 AF XY: 0.134 AC XY: 9960 AN XY: 74454

African (AFR) AF: 0.147 AC: 6103 AN: 41560

American (AMR) AF: 0.0969 AC: 1481 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3468

East Asian (EAS) AF: 0.0761 AC: 395 AN: 5188

South Asian (SAS) AF: 0.166 AC: 801 AN: 4824

European-Finnish (FIN) AF: 0.162 AC: 1719 AN: 10592

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8636 AN: 68020

Other (OTH) AF: 0.123 AC: 260 AN: 2110

Alfa AF: 0.128 Hom.: 2245

Bravo AF: 0.125

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.66
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6060239; hg19: chr20-33694580;