12-87537289-C-T

Variant names:

• chr12-87537289-C-T
• rs11104542

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 0.146 in 152,012 control chromosomes in the GnomAD database, including 2,087 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 (2087 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.296 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: 0.146 AC: 22179 AN: 151894 Hom.: 2085 Cov.: 31

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.146 AC: 22187 AN: 152012 Hom.: 2087 Cov.: 31 AF XY: 0.149 AC XY: 11096 AN XY: 74292

African (AFR) AF: 0.0387 AC: 1604 AN: 41498

American (AMR) AF: 0.177 AC: 2701 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1589 AN: 5144

South Asian (SAS) AF: 0.286 AC: 1375 AN: 4816

European-Finnish (FIN) AF: 0.165 AC: 1736 AN: 10552

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11983 AN: 67958

Other (OTH) AF: 0.147 AC: 311 AN: 2114

Alfa AF: 0.147 Hom.: 2827

Bravo AF: 0.138

Asia WGS AF: 0.270 AC: 940 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	0.89
DANN	Benign	0.34
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs11104542; hg19: chr12-87931066;