rs12230223

Variant names:

• chr12-91068951-T-C
• rs12230223

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.137 AC: 5666 AN: 41440

American (AMR) AF: 0.167 AC: 2547 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3460

East Asian (EAS) AF: 0.250 AC: 1284 AN: 5126

South Asian (SAS) AF: 0.139 AC: 666 AN: 4808

European-Finnish (FIN) AF: 0.220 AC: 2321 AN: 10544

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12655 AN: 67908

Other (OTH) AF: 0.190 AC: 400 AN: 2100

Alfa AF: 0.183 Hom.: 7254

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs12230223; hg19: chr12-91462728;