rs10886221

Variant names:

• chr10-83374200-C-T
• rs10886221

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.520 AC: 21554 AN: 41412

American (AMR) AF: 0.348 AC: 5296 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 914 AN: 3466

East Asian (EAS) AF: 0.220 AC: 1134 AN: 5152

South Asian (SAS) AF: 0.346 AC: 1668 AN: 4820

European-Finnish (FIN) AF: 0.310 AC: 3276 AN: 10572

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19327 AN: 67922

Other (OTH) AF: 0.302 AC: 639 AN: 2114

Alfa AF: 0.304 Hom.: 12446

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
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10886221; hg19: chr10-85133956;