rs4560089

Variant names:

• chr2-35475822-C-T
• rs4560089

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 0.42 in 151,900 control chromosomes in the GnomAD database, including 14,241 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 0.42 (14241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63703 AN: 151784 Hom.: 14217 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.420 AC: 63768 AN: 151900 Hom.: 14241 Cov.: 32 AF XY: 0.428 AC XY: 31796 AN XY: 74242

African (AFR) AF: 0.484 AC: 20051 AN: 41396

American (AMR) AF: 0.505 AC: 7699 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3470

East Asian (EAS) AF: 0.780 AC: 4026 AN: 5162

South Asian (SAS) AF: 0.422 AC: 2029 AN: 4808

European-Finnish (FIN) AF: 0.432 AC: 4555 AN: 10550

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23121 AN: 67944

Other (OTH) AF: 0.414 AC: 872 AN: 2108

Alfa AF: 0.368 Hom.: 45141

Bravo AF: 0.431

Asia WGS AF: 0.577 AC: 2004 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.55
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs4560089; hg19: chr2-35700888;