rs12219125

Variant names:

• chr10-20304158-G-T
• rs12219125

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 0.145 in 151,608 control chromosomes in the GnomAD database, including 1,634 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 0.15 (1634 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 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: 0.145 AC: 22025 AN: 151490 Hom.: 1634 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0928

Gnomad SAS AF: 0.0471

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.145 AC: 22039 AN: 151608 Hom.: 1634 Cov.: 31 AF XY: 0.145 AC XY: 10745 AN XY: 74022

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0930

Gnomad4 SAS AF: 0.0475

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.139

Alfa AF: 0.144 Hom.: 3513

Bravo AF: 0.144

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12219125; hg19: chr10-20593087;