rs10886221

chr10-83374200-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.357 in 151,890 control chromosomes in the GnomAD database, including 10,704 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 0.36 (10704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 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: 0.357 AC: 54199 AN: 151772 Hom.: 10665 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.357 AC: 54285 AN: 151890 Hom.: 10704 Cov.: 32 AF XY: 0.359 AC XY: 26661 AN XY: 74226

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.302

Alfa AF: 0.296 Hom.: 9301

Bravo AF: 0.366

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
Cadd	Benign	10
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10886221; hg19: chr10-85133956;