rs10832519

Variant names:

• chr11-15790384-T-C
• rs10832519

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 0.0467 in 152,164 control chromosomes in the GnomAD database, including 338 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 0.047 (338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 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: 0.0466 AC: 7085 AN: 152046 Hom.: 337 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.0787

Gnomad FIN AF: 0.0192

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0322

Gnomad OTH AF: 0.0585

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

GnomAD4 genome AF: 0.0467 AC: 7100 AN: 152164 Hom.: 338 Cov.: 32 AF XY: 0.0492 AC XY: 3659 AN XY: 74408

Gnomad4 AFR AF: 0.0293

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.0789

Gnomad4 FIN AF: 0.0192

Gnomad4 NFE AF: 0.0322

Gnomad4 OTH AF: 0.0584

Alfa AF: 0.0425 Hom.: 300

Bravo AF: 0.0545

Asia WGS AF: 0.116 AC: 402 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10832519; hg19: chr11-15811930;