rs4766200

Positions:

• chr12-4040383-A-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 0.169 in 151,820 control chromosomes in the GnomAD database, including 2,671 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 0.17 (2671 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4040383A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25604 AN: 151702 Hom.: 2652 Cov.: 28

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.169 AC: 25656 AN: 151820 Hom.: 2671 Cov.: 28 AF XY: 0.170 AC XY: 12612 AN XY: 74184

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.164

Alfa AF: 0.168 Hom.: 3322

Bravo AF: 0.184

Asia WGS AF: 0.332 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4766200; hg19: chr12-4149549;