rs10826223

Variant names:

• chr10-46056997-C-T
• rs10826223

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 0.124 in 151,884 control chromosomes in the GnomAD database, including 1,433 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 0.12 (1433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18773 AN: 151768 Hom.: 1431 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.0795

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0880

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.124 AC: 18784 AN: 151884 Hom.: 1433 Cov.: 32 AF XY: 0.126 AC XY: 9332 AN XY: 74242

African (AFR) AF: 0.143 AC: 5912 AN: 41354

American (AMR) AF: 0.219 AC: 3335 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0795 AC: 276 AN: 3470

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5162

South Asian (SAS) AF: 0.0880 AC: 424 AN: 4816

European-Finnish (FIN) AF: 0.122 AC: 1289 AN: 10542

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.105 AC: 7124 AN: 67980

Other (OTH) AF: 0.119 AC: 252 AN: 2110

Alfa AF: 0.120 Hom.: 1331

Bravo AF: 0.134

Asia WGS AF: 0.0460 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.79
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10826223; hg19: chr10-51538825;