10-88106892-C-T

Variant names:

• chr10-88106892-C-T
• rs11202656

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 0.249 in 152,086 control chromosomes in the GnomAD database, including 5,117 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 0.25 (5117 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 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: 0.250 AC: 37945 AN: 151968 Hom.: 5119 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.249 AC: 37943 AN: 152086 Hom.: 5117 Cov.: 33 AF XY: 0.252 AC XY: 18735 AN XY: 74336

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.243

Alfa AF: 0.272 Hom.: 11888

Bravo AF: 0.239

Asia WGS AF: 0.349 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.66
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11202656; hg19: chr10-89866649;