rs10899234

Variant names:

• chr11-76577893-G-A
• rs10899234

Your query was ambiguous. Multiple possible variants found:

• chr11-76577893-G-A
• chr11-76577893-G-T

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 0.385 in 152,120 control chromosomes in the GnomAD database, including 12,151 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 0.39 (12151 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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: 0.385 AC: 58523 AN: 152002 Hom.: 12133 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.385 AC: 58595 AN: 152120 Hom.: 12151 Cov.: 33 AF XY: 0.381 AC XY: 28349 AN XY: 74372

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.352

Alfa AF: 0.345 Hom.: 13214

Bravo AF: 0.385

Asia WGS AF: 0.260 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10899234; hg19: chr11-76288937;