rs2251530

Variant names:

• chr9-84198025-A-G
• rs2251530

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 0.688 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.716 AC: 29665 AN: 41452

American (AMR) AF: 0.547 AC: 8357 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2596 AN: 3466

East Asian (EAS) AF: 0.496 AC: 2569 AN: 5176

South Asian (SAS) AF: 0.562 AC: 2707 AN: 4816

European-Finnish (FIN) AF: 0.685 AC: 7246 AN: 10580

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49204 AN: 67990

Other (OTH) AF: 0.694 AC: 1462 AN: 2108

Alfa AF: 0.710 Hom.: 65454

Bravo AF: 0.681

Asia WGS AF: 0.570 AC: 1981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.48
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2251530; hg19: chr9-86812940;