rs11999802

Variant names:

• chr9-5189773-T-G
• rs11999802

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 0.328 in 152,108 control chromosomes in the GnomAD database, including 9,182 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 0.33 (9182 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.328 AC: 49834 AN: 151990 Hom.: 9169 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.328 AC: 49895 AN: 152108 Hom.: 9182 Cov.: 33 AF XY: 0.330 AC XY: 24505 AN XY: 74364

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.301

Alfa AF: 0.253 Hom.: 6643

Bravo AF: 0.327

Asia WGS AF: 0.318 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11999802; hg19: chr9-5189773; COSMIC: COSV67562738;