rs10822136

Variant names:

• chr10-63112651-C-T
• rs10822136

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 0.257 in 151,868 control chromosomes in the GnomAD database, including 5,234 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 0.26 (5234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39073 AN: 151750 Hom.: 5231 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.257 AC: 39083 AN: 151868 Hom.: 5234 Cov.: 32 AF XY: 0.257 AC XY: 19106 AN XY: 74210

African (AFR) AF: 0.299 AC: 12378 AN: 41396

American (AMR) AF: 0.338 AC: 5150 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3470

East Asian (EAS) AF: 0.0969 AC: 501 AN: 5168

South Asian (SAS) AF: 0.341 AC: 1646 AN: 4824

European-Finnish (FIN) AF: 0.204 AC: 2153 AN: 10530

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15598 AN: 67906

Other (OTH) AF: 0.248 AC: 524 AN: 2116

Alfa AF: 0.256 Hom.: 2991

Bravo AF: 0.265

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.6
DANN	Benign	0.64
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs10822136; hg19: chr10-64872411;