rs4560089

Variant names:

• chr2-35475822-C-T
• rs4560089

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.420 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

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.414

Alfa AF: 0.358 Hom.: 20384

Bravo AF: 0.431

Asia WGS AF: 0.577 AC: 2004 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	2.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4560089; hg19: chr2-35700888;