rs11611206

Positions:

• chr12-68274666-G-A
• chr12-68274666-G-T

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 0.154 in 152,110 control chromosomes in the GnomAD database, including 1,884 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 0.15 (1884 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

MDM1 (HGNC:29917): (Mdm1 nuclear protein) This gene encodes a microtubule-binding nuclear protein that localizes to the centrioles of dividing cells and differentiating multiciliated cells and negatively regulates centriole duplication. The encoded protein is closely associated with the centriole barrel, and resides in the centriole lumen. Naturally-occurring mutations in the orthologous mouse gene are associated with age-related retinal degeneration. [provided by RefSeq, Feb 2019]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68274666G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MDM1	ENST00000357874.3	n.*212-2134C>T		intron_variant		5		ENSP00000350544.3

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23384 AN: 151990 Hom.: 1884 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.154 AC: 23384 AN: 152110 Hom.: 1884 Cov.: 32 AF XY: 0.157 AC XY: 11701 AN XY: 74330

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0911

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.156

Alfa AF: 0.0713 Hom.: 82

Bravo AF: 0.149

Asia WGS AF: 0.0980 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
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: rs11611206; hg19: chr12-68668446;