rs9300826

Variant names:

• chr13-103550825-G-A
• rs9300826

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 0.0858 in 152,020 control chromosomes in the GnomAD database, including 895 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 0.086 (895 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

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 (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0859 AC: 13045 AN: 151902 Hom.: 895 Cov.: 33

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0326

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0704

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

GnomAD4 genome AF: 0.0858 AC: 13045 AN: 152020 Hom.: 895 Cov.: 33 AF XY: 0.0899 AC XY: 6679 AN XY: 74266

Gnomad4 AFR AF: 0.0214

Gnomad4 AMR AF: 0.0518

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0332

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0692

Alfa AF: 0.0966 Hom.: 393

Bravo AF: 0.0687

Asia WGS AF: 0.0800 AC: 276 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9300826; hg19: chr13-104203175;