chr20-7829452-A-G

Variant names:

• chr20-7829452-A-G
• rs10485717

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 0.342 in 151,956 control chromosomes in the GnomAD database, including 10,117 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 0.34 (10117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.515 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: 0.342 AC: 51866 AN: 151836 Hom.: 10085 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.342 AC: 51957 AN: 151956 Hom.: 10117 Cov.: 32 AF XY: 0.339 AC XY: 25216 AN XY: 74276

African (AFR) AF: 0.521 AC: 21582 AN: 41460

American (AMR) AF: 0.328 AC: 5004 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1174 AN: 3462

East Asian (EAS) AF: 0.324 AC: 1676 AN: 5170

South Asian (SAS) AF: 0.488 AC: 2341 AN: 4802

European-Finnish (FIN) AF: 0.205 AC: 2169 AN: 10572

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16914 AN: 67932

Other (OTH) AF: 0.354 AC: 746 AN: 2110

Alfa AF: 0.277 Hom.: 12156

Bravo AF: 0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.62
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs10485717; hg19: chr20-7810099;