rs2251530

chr9-84198025-A-G

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 0.688 in 152,056 control chromosomes in the GnomAD database, including 36,427 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 0.69 (36427 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104576 AN: 151938 Hom.: 36403 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.688 AC: 104640 AN: 152056 Hom.: 36427 Cov.: 32 AF XY: 0.681 AC XY: 50648 AN XY: 74334

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.694

Alfa AF: 0.713 Hom.: 52031

Bravo AF: 0.681

Asia WGS AF: 0.570 AC: 1981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.95
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2251530; hg19: chr9-86812940;