rs13068893

Variant names:

• chr3-122307242-C-G
• rs13068893

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 0.0944 in 152,218 control chromosomes in the GnomAD database, including 1,252 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 0.094 (1252 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 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: 0.0943 AC: 14337 AN: 152100 Hom.: 1240 Cov.: 33

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0479

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.0944 AC: 14369 AN: 152218 Hom.: 1252 Cov.: 33 AF XY: 0.0998 AC XY: 7424 AN XY: 74424

Gnomad4 AFR AF: 0.0367

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.0479

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0796

Gnomad4 OTH AF: 0.0881

Alfa AF: 0.0846 Hom.: 84

Bravo AF: 0.0947

Asia WGS AF: 0.336 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
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: rs13068893; hg19: chr3-122026089;