rs9318166

Variant names:

• chr13-73349748-G-A
• rs9318166

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 0.259 in 151,898 control chromosomes in the GnomAD database, including 5,457 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 0.26 (5457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 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: 0.259 AC: 39330 AN: 151778 Hom.: 5449 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.259 AC: 39362 AN: 151898 Hom.: 5457 Cov.: 32 AF XY: 0.260 AC XY: 19333 AN XY: 74238

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.255

Alfa AF: 0.225 Hom.: 5057

Bravo AF: 0.266

Asia WGS AF: 0.236 AC: 819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9318166; hg19: chr13-73923885; COSMIC: COSV69363903;