12-84537618-T-G

Position:

• chr12-84537618-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.519

Alfa AF: 0.572 Hom.: 41437

Bravo AF: 0.528

Asia WGS AF: 0.587 AC: 2030 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2611279; hg19: chr12-84931397;