rs2899109

Variant names:

• chr4-58123846-A-C
• rs2899109

Your query was ambiguous. Multiple possible variants found:

• chr4-58123846-A-C
• chr4-58123846-A-G

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 0.399 in 151,810 control chromosomes in the GnomAD database, including 12,685 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 0.40 (12685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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: 0.399 AC: 60477 AN: 151692 Hom.: 12668 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.399 AC: 60535 AN: 151810 Hom.: 12685 Cov.: 31 AF XY: 0.397 AC XY: 29430 AN XY: 74188

African (AFR) AF: 0.548 AC: 22676 AN: 41388

American (AMR) AF: 0.360 AC: 5490 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1340 AN: 3466

East Asian (EAS) AF: 0.277 AC: 1429 AN: 5162

South Asian (SAS) AF: 0.369 AC: 1772 AN: 4808

European-Finnish (FIN) AF: 0.361 AC: 3802 AN: 10534

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22671 AN: 67906

Other (OTH) AF: 0.401 AC: 840 AN: 2096

Alfa AF: 0.357 Hom.: 2587

Bravo AF: 0.407

Asia WGS AF: 0.332 AC: 1156 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2899109; hg19: chr4-58990012;