rs2125716

Variant names:

• chr12-84547650-A-G
• rs2125716

Your query was ambiguous. Multiple possible variants found:

• chr12-84547650-A-G
• chr12-84547650-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 0.81 in 152,084 control chromosomes in the GnomAD database, including 50,326 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 0.81 (50326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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: 0.811 AC: 123173 AN: 151966 Hom.: 50289 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.810 AC: 123261 AN: 152084 Hom.: 50326 Cov.: 32 AF XY: 0.812 AC XY: 60330 AN XY: 74334

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.769

Alfa AF: 0.761 Hom.: 56226

Bravo AF: 0.804

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2125716; hg19: chr12-84941429;