rs10826548

Variant names:

• chr10-28966665-C-A
• rs10826548

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 0.137 in 152,110 control chromosomes in the GnomAD database, including 2,121 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 0.14 (2121 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 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: 0.137 AC: 20862 AN: 151992 Hom.: 2116 Cov.: 32

Gnomad AFR AF: 0.0363

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.137 AC: 20870 AN: 152110 Hom.: 2121 Cov.: 32 AF XY: 0.141 AC XY: 10482 AN XY: 74358

African (AFR) AF: 0.0361 AC: 1500 AN: 41508

American (AMR) AF: 0.164 AC: 2499 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3472

East Asian (EAS) AF: 0.501 AC: 2583 AN: 5154

South Asian (SAS) AF: 0.297 AC: 1428 AN: 4814

European-Finnish (FIN) AF: 0.133 AC: 1404 AN: 10584

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10431 AN: 67984

Other (OTH) AF: 0.162 AC: 342 AN: 2106

Alfa AF: 0.138 Hom.: 203

Bravo AF: 0.135

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.45
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10826548; hg19: chr10-29255594;