rs12412241

Variant names:

• chr10-8085176-G-A
• rs12412241

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 0.295 in 152,028 control chromosomes in the GnomAD database, including 6,899 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 0.29 (6899 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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: 0.295 AC: 44748 AN: 151910 Hom.: 6885 Cov.: 33

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.295 AC: 44792 AN: 152028 Hom.: 6899 Cov.: 33 AF XY: 0.292 AC XY: 21713 AN XY: 74300

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.274

Alfa AF: 0.278 Hom.: 3429

Bravo AF: 0.309

Asia WGS AF: 0.165 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12412241; hg19: chr10-8127139;