rs973328

Variant names:

• chr12-68294126-C-G
• rs973328
• ENST00000357874.3:n.57+1139G>C

Your query was ambiguous. Multiple possible variants found:

• chr12-68294126-C-G
• chr12-68294126-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000357874.3(MDM1):​n.57+1139G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,054 control chromosomes in the GnomAD database, including 8,321 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 0.31 (8321 hom., cov: 33)
• Consequence: MDM1 ENST00000357874.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 4 publications found

Genes affected

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]

MDM1 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000303715 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MDM1	ENST00000357874.3	n.57+1139G>C		intron_variant	Intron 1 of 3	5		ENSP00000350544.3
ENSG00000303715	ENST00000796708.1	n.135-18288C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46573 AN: 151936 Hom.: 8319 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.306 AC: 46588 AN: 152054 Hom.: 8321 Cov.: 33 AF XY: 0.314 AC XY: 23322 AN XY: 74314

African (AFR) AF: 0.147 AC: 6110 AN: 41492

American (AMR) AF: 0.375 AC: 5718 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 911 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1064 AN: 5172

South Asian (SAS) AF: 0.203 AC: 980 AN: 4824

European-Finnish (FIN) AF: 0.538 AC: 5673 AN: 10546

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24887 AN: 67964

Other (OTH) AF: 0.298 AC: 629 AN: 2114

Alfa AF: 0.215 Hom.: 549

Bravo AF: 0.290

Asia WGS AF: 0.192 AC: 665 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.44
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs973328; hg19: chr12-68687906; COSMIC: COSV107320704;