rs925825

Variant names:

• chr2-188883920-A-G
• rs925825

Your query was ambiguous. Multiple possible variants found:

• chr2-188883920-A-G
• chr2-188883920-A-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 0.302 in 151,936 control chromosomes in the GnomAD database, including 8,168 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 0.30 (8168 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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: 0.302 AC: 45860 AN: 151818 Hom.: 8160 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.302 AC: 45864 AN: 151936 Hom.: 8168 Cov.: 31 AF XY: 0.306 AC XY: 22700 AN XY: 74246

African (AFR) AF: 0.103 AC: 4267 AN: 41510

American (AMR) AF: 0.340 AC: 5197 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1007 AN: 3464

East Asian (EAS) AF: 0.471 AC: 2419 AN: 5138

South Asian (SAS) AF: 0.415 AC: 1998 AN: 4810

European-Finnish (FIN) AF: 0.410 AC: 4325 AN: 10540

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25571 AN: 67886

Other (OTH) AF: 0.299 AC: 632 AN: 2112

Alfa AF: 0.345 Hom.: 11919

Bravo AF: 0.285

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs925825; hg19: chr2-189748646;