rs10850145

Variant names:

• chr12-113506324-C-T
• rs10850145

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 0.157 in 151,884 control chromosomes in the GnomAD database, including 2,627 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 0.16 (2627 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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: 0.157 AC: 23823 AN: 151768 Hom.: 2615 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.0798

Gnomad FIN AF: 0.0687

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.157 AC: 23868 AN: 151884 Hom.: 2627 Cov.: 31 AF XY: 0.154 AC XY: 11423 AN XY: 74246

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.0896

Gnomad4 SAS AF: 0.0800

Gnomad4 FIN AF: 0.0687

Gnomad4 NFE AF: 0.0966

Gnomad4 OTH AF: 0.148

Alfa AF: 0.113 Hom.: 593

Bravo AF: 0.170

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10850145; hg19: chr12-113944129;