rs13068893

Variant names:

• chr3-122307242-C-G
• rs13068893

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0367 AC: 1526 AN: 41524

American (AMR) AF: 0.175 AC: 2669 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0479 AC: 166 AN: 3468

East Asian (EAS) AF: 0.427 AC: 2208 AN: 5174

South Asian (SAS) AF: 0.231 AC: 1115 AN: 4822

European-Finnish (FIN) AF: 0.100 AC: 1066 AN: 10608

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0796 AC: 5411 AN: 68010

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs13068893; hg19: chr3-122026089;