rs11313889

Positions:

• chr12-12353249-GT-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (31663 hom., cov: 0)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12353250delT		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96952 AN: 151942 Hom.: 31655 Cov.: 0

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.638 AC: 97008 AN: 152060 Hom.: 31663 Cov.: 0 AF XY: 0.646 AC XY: 48015 AN XY: 74324

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.677

Alfa AF: 0.648 Hom.: 3889

Bravo AF: 0.641

Asia WGS AF: 0.783 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11313889; hg19: chr12-12506183;