rs9299952

Variant names:

• chr11-19096914-G-A
• rs9299952

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 0.0941 in 152,194 control chromosomes in the GnomAD database, including 815 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 0.094 (815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

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 (NFE) allele frequency at 95% confidence interval = 0.112 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: 0.0941 AC: 14303 AN: 152076 Hom.: 815 Cov.: 32

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0941 AC: 14314 AN: 152194 Hom.: 815 Cov.: 32 AF XY: 0.0968 AC XY: 7200 AN XY: 74402

Gnomad4 AFR AF: 0.0508

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.0882

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0834

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0899

Alfa AF: 0.107 Hom.: 433

Bravo AF: 0.0832

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9299952; hg19: chr11-19118461;