10-20691087-G-A

Variant names:

• chr10-20691087-G-A
• rs9645521

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 0.382 in 151,650 control chromosomes in the GnomAD database, including 11,803 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 0.38 (11803 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 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: 0.382 AC: 57856 AN: 151532 Hom.: 11769 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.382 AC: 57939 AN: 151650 Hom.: 11803 Cov.: 31 AF XY: 0.376 AC XY: 27874 AN XY: 74104

African (AFR) AF: 0.534 AC: 22031 AN: 41282

American (AMR) AF: 0.316 AC: 4819 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3466

East Asian (EAS) AF: 0.269 AC: 1381 AN: 5126

South Asian (SAS) AF: 0.321 AC: 1541 AN: 4798

European-Finnish (FIN) AF: 0.242 AC: 2552 AN: 10538

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.339 AC: 23009 AN: 67896

Other (OTH) AF: 0.412 AC: 866 AN: 2102

Alfa AF: 0.353 Hom.: 15840

Bravo AF: 0.396

Asia WGS AF: 0.335 AC: 1163 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.70
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs9645521; hg19: chr10-20980016;