rs12125250

Variant names:

• chr1-188410297-C-A
• rs12125250

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 0.223 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.134 AC: 5546 AN: 41382

American (AMR) AF: 0.188 AC: 2850 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 747 AN: 3448

East Asian (EAS) AF: 0.212 AC: 1086 AN: 5132

South Asian (SAS) AF: 0.407 AC: 1959 AN: 4808

European-Finnish (FIN) AF: 0.290 AC: 3047 AN: 10524

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17661 AN: 67618

Other (OTH) AF: 0.215 AC: 452 AN: 2102

Alfa AF: 0.248 Hom.: 17897

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
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs12125250; hg19: chr1-188379428;