rs6013355

Variant names:

• chr20-52021121-A-G
• rs6013355

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 0.216 in 152,088 control chromosomes in the GnomAD database, including 4,279 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 0.22 (4279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 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: 0.216 AC: 32787 AN: 151970 Hom.: 4272 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.216 AC: 32821 AN: 152088 Hom.: 4279 Cov.: 32 AF XY: 0.215 AC XY: 15976 AN XY: 74358

African (AFR) AF: 0.370 AC: 15324 AN: 41450

American (AMR) AF: 0.169 AC: 2585 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1386 AN: 5166

South Asian (SAS) AF: 0.117 AC: 564 AN: 4822

European-Finnish (FIN) AF: 0.173 AC: 1831 AN: 10596

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10111 AN: 67998

Other (OTH) AF: 0.191 AC: 403 AN: 2108

Alfa AF: 0.169 Hom.: 11220

Bravo AF: 0.224

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	10
DANN	Benign	0.91
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6013355; hg19: chr20-50637660;