rs9299952

chr11-19096914-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;