rs11203032

Variant names:

• chr10-89204857-T-G
• rs11203032

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;