rs12258125

Positions:

• chr10-36853420-C-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 0.398 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;