rs11788458

chr9-111855741-A-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 0.142 in 152,156 control chromosomes in the GnomAD database, including 1,597 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 0.14 (1597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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: 0.142 AC: 21602 AN: 152038 Hom.: 1597 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.142 AC: 21619 AN: 152156 Hom.: 1597 Cov.: 32 AF XY: 0.140 AC XY: 10390 AN XY: 74388

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0939

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0239

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.128

Alfa AF: 0.142 Hom.: 780

Bravo AF: 0.140

Asia WGS AF: 0.0800 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.3
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11788458; hg19: chr9-114618021;