rs13290397

chr9-78768538-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 0.112 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;