chr12-84537618-T-G

Variant names:

• chr12-84537618-T-G
• rs2611279

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 0.547 in 151,240 control chromosomes in the GnomAD database, including 23,448 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 0.55 (23448 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 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: 0.548 AC: 82760 AN: 151122 Hom.: 23447 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.547 AC: 82803 AN: 151240 Hom.: 23448 Cov.: 31 AF XY: 0.551 AC XY: 40727 AN XY: 73968

African (AFR) AF: 0.434 AC: 17956 AN: 41380

American (AMR) AF: 0.504 AC: 7641 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1604 AN: 3448

East Asian (EAS) AF: 0.767 AC: 3957 AN: 5158

South Asian (SAS) AF: 0.430 AC: 2074 AN: 4820

European-Finnish (FIN) AF: 0.703 AC: 7425 AN: 10556

Middle Eastern (MID) AF: 0.427 AC: 123 AN: 288

European-Non Finnish (NFE) AF: 0.599 AC: 40373 AN: 67408

Other (OTH) AF: 0.519 AC: 1091 AN: 2102

Alfa AF: 0.566 Hom.: 61553

Bravo AF: 0.528

Asia WGS AF: 0.587 AC: 2030 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.17
DANN	Benign	0.63
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2611279; hg19: chr12-84931397;