chr12-84627748-G-A

Position:

• chr12-84627748-G-A

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 0.0264 in 152,152 control chromosomes in the GnomAD database, including 108 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 0.026 (108 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.84627748G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0263 AC: 4005 AN: 152034 Hom.: 107 Cov.: 32

Gnomad AFR AF: 0.0273

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.00721

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.0353

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00962

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0264 AC: 4010 AN: 152152 Hom.: 108 Cov.: 32 AF XY: 0.0287 AC XY: 2133 AN XY: 74370

Gnomad4 AFR AF: 0.0273

Gnomad4 AMR AF: 0.0641

Gnomad4 ASJ AF: 0.00721

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0341

Gnomad4 FIN AF: 0.0353

Gnomad4 NFE AF: 0.00962

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.00655 Hom.: 1

Bravo AF: 0.0301

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506909; hg19: chr12-85021527;