12-4889370-C-G

Position:

• chr12-4889370-C-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 0.105 in 151,748 control chromosomes in the GnomAD database, including 1,238 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 0.11 (1238 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4889370C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15977 AN: 151632 Hom.: 1233 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0632

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.0609

Gnomad NFE AF: 0.0400

Gnomad OTH AF: 0.0964

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

GnomAD4 genome AF: 0.105 AC: 16007 AN: 151748 Hom.: 1238 Cov.: 33 AF XY: 0.108 AC XY: 8003 AN XY: 74168

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0632

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.0459

Gnomad4 FIN AF: 0.0991

Gnomad4 NFE AF: 0.0400

Gnomad4 OTH AF: 0.0968

Alfa AF: 0.0754 Hom.: 104

Bravo AF: 0.111

Asia WGS AF: 0.140 AC: 484 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.55
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11063387; hg19: chr12-4998536;