chr12-28000594-T-C

Variant names:

• chr12-28000594-T-C
• rs2737447

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 0.0853 in 152,196 control chromosomes in the GnomAD database, including 702 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 0.085 (702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 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: 0.0854 AC: 12980 AN: 152078 Hom.: 702 Cov.: 32

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0853 AC: 12980 AN: 152196 Hom.: 702 Cov.: 32 AF XY: 0.0832 AC XY: 6189 AN XY: 74420

African (AFR) AF: 0.0221 AC: 917 AN: 41540

American (AMR) AF: 0.0774 AC: 1182 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0919 AC: 319 AN: 3472

East Asian (EAS) AF: 0.191 AC: 990 AN: 5172

South Asian (SAS) AF: 0.130 AC: 624 AN: 4808

European-Finnish (FIN) AF: 0.0701 AC: 744 AN: 10610

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7901 AN: 67998

Other (OTH) AF: 0.0761 AC: 161 AN: 2116

Alfa AF: 0.108 Hom.: 425

Bravo AF: 0.0840

Asia WGS AF: 0.138 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.30
DANN	Benign	0.58
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2737447; hg19: chr12-28153527;