12-112899358-A-G

Position:

• chr12-112899358-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 0.734 in 151,776 control chromosomes in the GnomAD database, including 41,940 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 0.73 (41940 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.112899358A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111272 AN: 151658 Hom.: 41931 Cov.: 29

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.734 AC: 111331 AN: 151776 Hom.: 41940 Cov.: 29 AF XY: 0.739 AC XY: 54765 AN XY: 74154

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.752

Alfa AF: 0.775 Hom.: 47400

Bravo AF: 0.732

Asia WGS AF: 0.822 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492028; hg19: chr12-113337163;