rs13067306

Variant names:

• chr3-94524869-G-A
• rs13067306

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 0.165 in 151,814 control chromosomes in the GnomAD database, including 2,402 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 0.17 (2402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 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: 0.165 AC: 25074 AN: 151720 Hom.: 2405 Cov.: 32

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.0584

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.165 AC: 25072 AN: 151814 Hom.: 2402 Cov.: 32 AF XY: 0.165 AC XY: 12223 AN XY: 74144

Gnomad4 AFR AF: 0.0850

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0203

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.149

Alfa AF: 0.194 Hom.: 3356

Bravo AF: 0.158

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13067306; hg19: chr3-94243713;