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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.0542

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0906

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0899 Hom.: 467

Bravo AF: 0.149

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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