rs2890489

Variant names:

• chr2-15583481-G-A
• rs2890489

Your query was ambiguous. Multiple possible variants found:

• chr2-15583481-G-A
• chr2-15583481-G-C
• chr2-15583481-G-T

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 0.661 in 149,512 control chromosomes in the GnomAD database, including 32,536 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 0.66 (32536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

ACMG classification

Verdict is Benign. Variant got -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 = 0.766 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: 0.661 AC: 98719 AN: 149400 Hom.: 32513 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.661 AC: 98798 AN: 149512 Hom.: 32536 Cov.: 32 AF XY: 0.658 AC XY: 48011 AN XY: 72944

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.638

Alfa AF: 0.601 Hom.: 10915

Bravo AF: 0.661

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.074
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2890489; hg19: chr2-15723605;