rs13290397

Variant names:

• chr9-78768538-C-G
• rs13290397

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 0.112 in 152,198 control chromosomes in the GnomAD database, including 1,113 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 0.11 (1113 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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: 0.112 AC: 17073 AN: 152080 Hom.: 1108 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0945

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

GnomAD4 genome AF: 0.112 AC: 17112 AN: 152198 Hom.: 1113 Cov.: 33 AF XY: 0.109 AC XY: 8086 AN XY: 74410

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.0613

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.0447

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0935

Alfa AF: 0.117 Hom.: 136

Bravo AF: 0.108

Asia WGS AF: 0.0330 AC: 114 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	1.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13290397; hg19: chr9-81383454;