rs6052778

Variant names:

• chr20-4708590-T-C
• rs6052778

Your query was ambiguous. Multiple possible variants found:

• chr20-4708590-T-C
• chr20-4708590-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 0.144 in 152,202 control chromosomes in the GnomAD database, including 2,059 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 0.14 (2059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.144 AC: 21882 AN: 152084 Hom.: 2035 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.0538

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0905

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.144 AC: 21972 AN: 152202 Hom.: 2059 Cov.: 32 AF XY: 0.145 AC XY: 10794 AN XY: 74422

African (AFR) AF: 0.273 AC: 11316 AN: 41492

American (AMR) AF: 0.133 AC: 2041 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3468

East Asian (EAS) AF: 0.0542 AC: 281 AN: 5188

South Asian (SAS) AF: 0.116 AC: 560 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1191 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0906 AC: 6160 AN: 68010

Other (OTH) AF: 0.122 AC: 257 AN: 2112

Alfa AF: 0.0927 Hom.: 566

Bravo AF: 0.149

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.60
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6052778; hg19: chr20-4689236; COSMIC: COSV56533085;