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. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.773 AC: 31127 AN: 40254

American (AMR) AF: 0.666 AC: 9996 AN: 15010

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2075 AN: 3416

East Asian (EAS) AF: 0.729 AC: 3391 AN: 4654

South Asian (SAS) AF: 0.751 AC: 3555 AN: 4732

European-Finnish (FIN) AF: 0.530 AC: 5520 AN: 10408

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.606 AC: 41067 AN: 67758

Other (OTH) AF: 0.638 AC: 1325 AN: 2076

Alfa AF: 0.641 Hom.: 21919

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
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2890489; hg19: chr2-15723605;