rs12335791

chr9-117758134-C-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 0.134 in 152,040 control chromosomes in the GnomAD database, including 1,727 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 0.13 (1727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 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: 0.134 AC: 20374 AN: 151924 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.134 AC: 20372 AN: 152040 Hom.: 1727 Cov.: 32 AF XY: 0.133 AC XY: 9893 AN XY: 74318

Gnomad4 AFR AF: 0.0550

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.138

Alfa AF: 0.159 Hom.: 267

Bravo AF: 0.126

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	15
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: rs12335791; hg19: chr9-120520412; COSMIC: COSV60396941; COSMIC: COSV60396941;