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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.302 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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.299

Alfa AF: 0.357 Hom.: 9418

Bravo AF: 0.285

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925825; hg19: chr2-189748646;