rs12472293

chr2-135890507-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 0.18 in 152,124 control chromosomes in the GnomAD database, including 2,829 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 0.18 (2829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

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 (SAS) allele frequency at 95% confidence interval = 0.276 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: 0.180 AC: 27374 AN: 152006 Hom.: 2832 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.180 AC: 27381 AN: 152124 Hom.: 2829 Cov.: 32 AF XY: 0.183 AC XY: 13620 AN XY: 74366

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.257

Alfa AF: 0.207 Hom.: 5919

Bravo AF: 0.182

Asia WGS AF: 0.219 AC: 762 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	4.7
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12472293; hg19: chr2-136648077;