chr10-87995886-C-T

Variant names:

• chr10-87995886-C-T
• rs11202614

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 0.142 in 152,052 control chromosomes in the GnomAD database, including 1,890 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 0.14 (1890 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 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: 0.142 AC: 21550 AN: 151934 Hom.: 1879 Cov.: 32

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.142 AC: 21584 AN: 152052 Hom.: 1890 Cov.: 32 AF XY: 0.142 AC XY: 10568 AN XY: 74318

Gnomad4 AFR AF: 0.0867

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.152

Alfa AF: 0.140 Hom.: 210

Bravo AF: 0.149

Asia WGS AF: 0.251 AC: 872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11202614; hg19: chr10-89755643;