20-7829733-A-G

Variant names:

• chr20-7829733-A-G
• rs6086234

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 0.354 in 152,108 control chromosomes in the GnomAD database, including 11,103 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 0.35 (11103 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.934
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 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: 0.353 AC: 53704 AN: 151992 Hom.: 11069 Cov.: 33

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.354 AC: 53802 AN: 152108 Hom.: 11103 Cov.: 33 AF XY: 0.351 AC XY: 26104 AN XY: 74358

African (AFR) AF: 0.562 AC: 23296 AN: 41486

American (AMR) AF: 0.332 AC: 5071 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1174 AN: 3464

East Asian (EAS) AF: 0.325 AC: 1682 AN: 5176

South Asian (SAS) AF: 0.488 AC: 2352 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2173 AN: 10590

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16933 AN: 67984

Other (OTH) AF: 0.365 AC: 769 AN: 2108

Alfa AF: 0.277 Hom.: 3571

Bravo AF: 0.372

Asia WGS AF: 0.457 AC: 1586 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.9
DANN	Benign	0.82
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs6086234; hg19: chr20-7810380;