rs9319109

Variant names:

• chr13-85038134-G-C
• rs9319109

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 0.371 in 151,856 control chromosomes in the GnomAD database, including 11,503 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 0.37 (11503 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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: 0.371 AC: 56311 AN: 151738 Hom.: 11483 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.371 AC: 56371 AN: 151856 Hom.: 11503 Cov.: 32 AF XY: 0.365 AC XY: 27075 AN XY: 74212

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.349

Alfa AF: 0.362 Hom.: 1302

Bravo AF: 0.373

Asia WGS AF: 0.242 AC: 837 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9319109; hg19: chr13-85612269;