rs13068298

Variant names:

• chr3-144053405-T-C
• rs13068298

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 0.322 in 152,082 control chromosomes in the GnomAD database, including 8,841 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 0.32 (8841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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: 0.322 AC: 48876 AN: 151966 Hom.: 8807 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.322 AC: 48942 AN: 152082 Hom.: 8841 Cov.: 32 AF XY: 0.321 AC XY: 23861 AN XY: 74374

African (AFR) AF: 0.497 AC: 20591 AN: 41452

American (AMR) AF: 0.249 AC: 3805 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3472

East Asian (EAS) AF: 0.197 AC: 1018 AN: 5176

South Asian (SAS) AF: 0.213 AC: 1027 AN: 4816

European-Finnish (FIN) AF: 0.280 AC: 2956 AN: 10574

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17648 AN: 67986

Other (OTH) AF: 0.316 AC: 667 AN: 2110

Alfa AF: 0.277 Hom.: 23402

Bravo AF: 0.328

Asia WGS AF: 0.211 AC: 733 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs13068298; hg19: chr3-143772247;