rs12258125

Variant names:

• chr10-36853420-C-T
• rs12258125

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 0.398 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.496 AC: 20526 AN: 41368

American (AMR) AF: 0.384 AC: 5865 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3472

East Asian (EAS) AF: 0.139 AC: 717 AN: 5156

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4812

European-Finnish (FIN) AF: 0.323 AC: 3408 AN: 10536

Middle Eastern (MID) AF: 0.317 AC: 92 AN: 290

European-Non Finnish (NFE) AF: 0.381 AC: 25902 AN: 67932

Other (OTH) AF: 0.366 AC: 770 AN: 2106

Alfa AF: 0.385 Hom.: 19329

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12258125; hg19: chr10-37142348;