10-59966393-G-A

Variant names:

• chr10-59966393-G-A
• rs9332447

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 0.343 in 151,890 control chromosomes in the GnomAD database, including 9,557 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 (9557 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 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: 0.343 AC: 52040 AN: 151768 Hom.: 9555 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.343 AC: 52082 AN: 151890 Hom.: 9557 Cov.: 32 AF XY: 0.338 AC XY: 25046 AN XY: 74208

African (AFR) AF: 0.252 AC: 10423 AN: 41420

American (AMR) AF: 0.291 AC: 4436 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1012 AN: 3472

East Asian (EAS) AF: 0.153 AC: 788 AN: 5164

South Asian (SAS) AF: 0.373 AC: 1796 AN: 4812

European-Finnish (FIN) AF: 0.340 AC: 3578 AN: 10516

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28629 AN: 67936

Other (OTH) AF: 0.378 AC: 796 AN: 2108

Alfa AF: 0.360 Hom.: 3317

Bravo AF: 0.333

Asia WGS AF: 0.307 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.1
DANN	Benign	0.71
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9332447; hg19: chr10-61726151;