10-110285084-TAAAACAAAAC-TAAAAC

Position:

• chr10-110285084-TAAAACAAAAC-TAAAAC

Variant summary

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

The NM_130439.3(MXI1):​c.*118_*122delAAAAC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 900,356 control chromosomes in the GnomAD database, including 107,123 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.44 (17448 hom., cov: 0)
  • Exomes 𝑓: 0.44 (89675 hom.)
• Consequence: MXI1 NM_130439.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

Genes affected

MXI1 (HGNC:7534): (MAX interactor 1, dimerization protein) Expression of the c-myc gene, which produces an oncogenic transcription factor, is tightly regulated in normal cells but is frequently deregulated in human cancers. The protein encoded by this gene is a transcriptional repressor thought to negatively regulate MYC function, and is therefore a potential tumor suppressor. This protein inhibits the transcriptional activity of MYC by competing for MAX, another basic helix-loop-helix protein that binds to MYC and is required for its function. Defects in this gene are frequently found in patients with prostate tumors. Three alternatively spliced transcripts encoding different isoforms have been described. Additional alternatively spliced transcripts may exist but the products of these transcripts have not been verified experimentally. [provided by RefSeq, Jul 2008]

MXI1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MXI1	NM_130439.3	c.*118_*122delAAAAC		3_prime_UTR_variant	6/6	ENST00000332674.9	NP_569157.2
MXI1	NM_005962.5	c.*118_*122delAAAAC		3_prime_UTR_variant	6/6		NP_005953.4
MXI1	NM_001008541.1	c.*118_*122delAAAAC		3_prime_UTR_variant	5/5		NP_001008541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MXI1	ENST00000332674.9	c.*118_*122delAAAAC		3_prime_UTR_variant	6/6	1	NM_130439.3	ENSP00000331152.5

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66476 AN: 151292 Hom.: 17448 Cov.: 0

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.453

GnomAD4 exome AF: 0.438 AC: 327877 AN: 748944 Hom.: 89675 AF XY: 0.442 AC XY: 165018 AN XY: 373294

Gnomad4 AFR exome AF: 0.0896

Gnomad4 AMR exome AF: 0.556

Gnomad4 ASJ exome AF: 0.452

Gnomad4 EAS exome AF: 0.816

Gnomad4 SAS exome AF: 0.490

Gnomad4 FIN exome AF: 0.535

Gnomad4 NFE exome AF: 0.421

Gnomad4 OTH exome AF: 0.435

GnomAD4 genome AF: 0.439 AC: 66477 AN: 151412 Hom.: 17448 Cov.: 0 AF XY: 0.450 AC XY: 33242 AN XY: 73918

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.449

Bravo AF: 0.427

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: rs16448; hg19: chr10-112044842;