rs6085533

Variant names:

• chr20-6394813-T-A
• rs6085533

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 0.294 in 152,080 control chromosomes in the GnomAD database, including 6,769 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 0.29 (6769 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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: 0.294 AC: 44736 AN: 151962 Hom.: 6770 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.294 AC: 44742 AN: 152080 Hom.: 6769 Cov.: 32 AF XY: 0.288 AC XY: 21369 AN XY: 74320

African (AFR) AF: 0.324 AC: 13441 AN: 41472

American (AMR) AF: 0.263 AC: 4010 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3468

East Asian (EAS) AF: 0.110 AC: 568 AN: 5178

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4826

European-Finnish (FIN) AF: 0.248 AC: 2626 AN: 10570

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20664 AN: 67986

Other (OTH) AF: 0.317 AC: 667 AN: 2106

Alfa AF: 0.297 Hom.: 795

Bravo AF: 0.294

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.85
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs6085533; hg19: chr20-6375460;