rs11999802

Positions:

• chr9-5189773-T-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;