rs12230223

chr12-91068951-T-C

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 0.174 in 151,852 control chromosomes in the GnomAD database, including 2,419 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 0.17 (2419 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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: 0.174 AC: 26367 AN: 151734 Hom.: 2422 Cov.: 30

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.174 AC: 26363 AN: 151852 Hom.: 2419 Cov.: 30 AF XY: 0.176 AC XY: 13065 AN XY: 74206

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.190

Alfa AF: 0.191 Hom.: 2831

Bravo AF: 0.169

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.0
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12230223; hg19: chr12-91462728;