rs11203032

Positions:

• chr10-89204857-T-G

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 0.135 in 152,234 control chromosomes in the GnomAD database, including 2,940 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 0.13 (2940 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.135 AC: 20516 AN: 152116 Hom.: 2929 Cov.: 33

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.135 AC: 20547 AN: 152234 Hom.: 2940 Cov.: 33 AF XY: 0.147 AC XY: 10926 AN XY: 74412

Gnomad4 AFR AF: 0.0247

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.138

Alfa AF: 0.123 Hom.: 2146

Bravo AF: 0.131

Asia WGS AF: 0.457 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11203032; hg19: chr10-90964614;