rs12258125

Variant names:

• chr10-36853420-C-T
• rs12258125

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 0.398 in 151,842 control chromosomes in the GnomAD database, including 12,455 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 0.40 (12455 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.398 AC: 60381 AN: 151722 Hom.: 12428 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.398 AC: 60447 AN: 151842 Hom.: 12455 Cov.: 31 AF XY: 0.392 AC XY: 29054 AN XY: 74196

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.366

Alfa AF: 0.381 Hom.: 15031

Bravo AF: 0.404

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12258125; hg19: chr10-37142348;