rs10832313

chr11-14900817-A-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 0.104 in 152,230 control chromosomes in the GnomAD database, including 1,080 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 0.10 (1080 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 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: 0.104 AC: 15746 AN: 152112 Hom.: 1077 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0656

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.104 AC: 15775 AN: 152230 Hom.: 1080 Cov.: 33 AF XY: 0.101 AC XY: 7503 AN XY: 74438

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.0655

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.0460

Gnomad4 SAS AF: 0.0667

Gnomad4 FIN AF: 0.0473

Gnomad4 NFE AF: 0.0759

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0823 Hom.: 226

Bravo AF: 0.110

Asia WGS AF: 0.0850 AC: 295 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.1
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: rs10832313; hg19: chr11-14922363;