chr20-6999988-G-T

Variant names:

• chr20-6999988-G-T
• rs6085820

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 0.0405 in 152,090 control chromosomes in the GnomAD database, including 140 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 0.040 (140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0581 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0405 AC: 6154 AN: 151972 Hom.: 140 Cov.: 32

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0187

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0405 AC: 6154 AN: 152090 Hom.: 140 Cov.: 32 AF XY: 0.0395 AC XY: 2933 AN XY: 74342

African (AFR) AF: 0.0178 AC: 740 AN: 41484

American (AMR) AF: 0.0314 AC: 480 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0259 AC: 90 AN: 3470

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5172

South Asian (SAS) AF: 0.0187 AC: 90 AN: 4802

European-Finnish (FIN) AF: 0.0542 AC: 573 AN: 10580

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0596 AC: 4052 AN: 67998

Other (OTH) AF: 0.0374 AC: 79 AN: 2114

Alfa AF: 0.0483 Hom.: 224

Bravo AF: 0.0382

Asia WGS AF: 0.0170 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.58
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs6085820; hg19: chr20-6980635;