rs9318166

chr13-73349748-G-A

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/exons	MANE	UniProt

Ensembl

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