chr3-189347367-A-C

Variant names:

• chr3-189347367-A-C
• rs13059863

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 0.341 in 151,968 control chromosomes in the GnomAD database, including 9,869 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 0.34 (9869 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.58
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.13).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 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: 0.341 AC: 51725 AN: 151850 Hom.: 9852 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.341 AC: 51788 AN: 151968 Hom.: 9869 Cov.: 32 AF XY: 0.339 AC XY: 25173 AN XY: 74254

African (AFR) AF: 0.513 AC: 21265 AN: 41418

American (AMR) AF: 0.265 AC: 4043 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3468

East Asian (EAS) AF: 0.518 AC: 2661 AN: 5140

South Asian (SAS) AF: 0.264 AC: 1272 AN: 4816

European-Finnish (FIN) AF: 0.248 AC: 2617 AN: 10570

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.260 AC: 17663 AN: 67964

Other (OTH) AF: 0.313 AC: 659 AN: 2108

Alfa AF: 0.288 Hom.: 31091

Bravo AF: 0.354

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.049
DANN	Benign	0.11
PhyloP100		-4.6

Splicing

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

Other links and lift over

dbSNP: rs13059863; hg19: chr3-189065156;