rs12472293

Variant names:

• chr2-135890507-T-C
• rs12472293

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 0.18 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.142 AC: 5884 AN: 41498

American (AMR) AF: 0.235 AC: 3589 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3466

East Asian (EAS) AF: 0.190 AC: 983 AN: 5170

South Asian (SAS) AF: 0.288 AC: 1388 AN: 4814

European-Finnish (FIN) AF: 0.138 AC: 1464 AN: 10592

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11680 AN: 68006

Other (OTH) AF: 0.257 AC: 543 AN: 2110

Alfa AF: 0.191 Hom.: 11541

Bravo AF: 0.182

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.75
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs12472293; hg19: chr2-136648077;