12-65976791-C-T

Variant names:

• chr12-65976791-C-T
• rs1480464

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 0.208 in 152,068 control chromosomes in the GnomAD database, including 4,440 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 0.21 (4440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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: 0.209 AC: 31694 AN: 151950 Hom.: 4443 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.208 AC: 31691 AN: 152068 Hom.: 4440 Cov.: 32 AF XY: 0.213 AC XY: 15844 AN XY: 74344

African (AFR) AF: 0.144 AC: 5960 AN: 41426

American (AMR) AF: 0.311 AC: 4756 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3472

East Asian (EAS) AF: 0.751 AC: 3885 AN: 5172

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4824

European-Finnish (FIN) AF: 0.157 AC: 1667 AN: 10586

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12410 AN: 67996

Other (OTH) AF: 0.215 AC: 453 AN: 2110

Alfa AF: 0.204 Hom.: 2194

Bravo AF: 0.222

Asia WGS AF: 0.459 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.29
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1480464; hg19: chr12-66370571;