rs10826548

chr10-28966665-C-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0361

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.162

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.28
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10826548; hg19: chr10-29255594;