12-82035813-C-T

Variant names:

• chr12-82035813-C-T
• rs1865155

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 0.276 in 151,576 control chromosomes in the GnomAD database, including 6,005 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 0.28 (6005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 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: 0.276 AC: 41729 AN: 151458 Hom.: 5990 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.276 AC: 41761 AN: 151576 Hom.: 6005 Cov.: 32 AF XY: 0.276 AC XY: 20435 AN XY: 74106

African (AFR) AF: 0.215 AC: 8918 AN: 41404

American (AMR) AF: 0.299 AC: 4530 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1083 AN: 3456

East Asian (EAS) AF: 0.161 AC: 832 AN: 5156

South Asian (SAS) AF: 0.291 AC: 1404 AN: 4820

European-Finnish (FIN) AF: 0.302 AC: 3182 AN: 10546

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20926 AN: 67728

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.287 Hom.: 926

Bravo AF: 0.270

Asia WGS AF: 0.216 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.44
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1865155; hg19: chr12-82429592;