rs10899234

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;