10-46068452-G-C

Variant names:

• chr10-46068452-G-C
• rs10826075

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 0.227 in 152,176 control chromosomes in the GnomAD database, including 3,948 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 0.23 (3948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34447 AN: 152056 Hom.: 3943 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.227 AC: 34476 AN: 152176 Hom.: 3948 Cov.: 33 AF XY: 0.227 AC XY: 16855 AN XY: 74392

African (AFR) AF: 0.184 AC: 7619 AN: 41510

American (AMR) AF: 0.242 AC: 3698 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1008 AN: 3468

East Asian (EAS) AF: 0.271 AC: 1404 AN: 5176

South Asian (SAS) AF: 0.245 AC: 1180 AN: 4824

European-Finnish (FIN) AF: 0.196 AC: 2075 AN: 10602

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16647 AN: 67994

Other (OTH) AF: 0.242 AC: 512 AN: 2112

Alfa AF: 0.109 Hom.: 154

Bravo AF: 0.227

Asia WGS AF: 0.247 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.6
DANN	Benign	0.82
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs10826075; hg19: chr10-51527370;