rs9299952

Variant names:

• chr11-19096914-G-A
• rs9299952

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0508 AC: 2111 AN: 41524

American (AMR) AF: 0.0826 AC: 1264 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0834 AC: 402 AN: 4818

European-Finnish (FIN) AF: 0.206 AC: 2179 AN: 10576

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7761 AN: 68012

Other (OTH) AF: 0.0899 AC: 190 AN: 2114

Alfa AF: 0.111 Hom.: 653

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs9299952; hg19: chr11-19118461;