rs12125250

chr1-188410297-C-A

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 0.223 in 151,348 control chromosomes in the GnomAD database, including 4,198 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 0.22 (4198 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 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: 0.223 AC: 33668 AN: 151230 Hom.: 4192 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.223 AC: 33687 AN: 151348 Hom.: 4198 Cov.: 31 AF XY: 0.225 AC XY: 16642 AN XY: 73920

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.215

Alfa AF: 0.256 Hom.: 7833

Bravo AF: 0.204

Asia WGS AF: 0.346 AC: 1204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.13
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12125250; hg19: chr1-188379428;