10-110285084-TAAAACAAAAC-TAAAACAAAACAAAAC

Position:

• chr10-110285084-TAAAACAAAAC-TAAAACAAAACAAAAC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_130439.3(MXI1):​c.*118_*122dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00051 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00043 (1 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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000508 (77/151542) while in subpopulation SAS AF= 0.00166 (8/4820). AF 95% confidence interval is 0.000825. There are 0 homozygotes in gnomad4. There are 49 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MXI1	NM_130439.3	c.*118_*122dup		3_prime_UTR_variant	6/6	ENST00000332674.9
MXI1	NM_001008541.1	c.*118_*122dup		3_prime_UTR_variant	5/5
MXI1	NM_005962.5	c.*118_*122dup		3_prime_UTR_variant	6/6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.000502 AC: 76 AN: 151422 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000968

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00336

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000384

Gnomad OTH AF: 0.000963

GnomAD4 exome AF: 0.000431 AC: 323 AN: 750032 Hom.: 1 Cov.: 0 AF XY: 0.000463 AC XY: 173 AN XY: 373882

Gnomad4 AFR exome AF: 0.0000931

Gnomad4 AMR exome AF: 0.0000774

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000144

Gnomad4 SAS exome AF: 0.00185

Gnomad4 FIN exome AF: 0.00198

Gnomad4 NFE exome AF: 0.000295

Gnomad4 OTH exome AF: 0.000347

GnomAD4 genome AF: 0.000508 AC: 77 AN: 151542 Hom.: 0 Cov.: 0 AF XY: 0.000662 AC XY: 49 AN XY: 74000

Gnomad4 AFR AF: 0.000121

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.00336

Gnomad4 NFE AF: 0.000384

Gnomad4 OTH AF: 0.000952

Bravo AF: 0.000230

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;