rs12412654

Variant names:

• chr10-32057822-G-C
• rs12412654

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 0.222 in 152,176 control chromosomes in the GnomAD database, including 3,916 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 (3916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 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: 0.222 AC: 33724 AN: 152058 Hom.: 3919 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.222 AC: 33729 AN: 152176 Hom.: 3916 Cov.: 32 AF XY: 0.225 AC XY: 16741 AN XY: 74420

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.230

Alfa AF: 0.227 Hom.: 492

Bravo AF: 0.219

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12412654; hg19: chr10-32346750; COSMIC: COSV56653525;