rs2089907

Variant names:

• chr2-2480398-T-A
• rs2089907

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 0.321 in 151,910 control chromosomes in the GnomAD database, including 10,146 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 0.32 (10146 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 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: 0.321 AC: 48652 AN: 151792 Hom.: 10123 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.321 AC: 48728 AN: 151910 Hom.: 10146 Cov.: 32 AF XY: 0.320 AC XY: 23797 AN XY: 74254

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.289

Alfa AF: 0.278 Hom.: 934

Bravo AF: 0.331

Asia WGS AF: 0.380 AC: 1310 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2089907; hg19: chr2-2484170;