chr10-110285084-T-TAAAAC

Variant names:

• chr10-110285084-T-TAAAAC
• rs16448
• NM_130439.3:c.*118_*122dupAAAAC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_130439.3(MXI1):​c.*118_*122dupAAAAC 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
• Publications: 5 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130439.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MXI1	NM_130439.3	MANE Select	c.*118_*122dupAAAAC		3_prime_UTR	Exon 6 of 6	NP_569157.2	P50539-3
	MXI1	NM_005962.5		c.*118_*122dupAAAAC		3_prime_UTR	Exon 6 of 6	NP_005953.4
	MXI1	NM_001008541.1		c.*118_*122dupAAAAC		3_prime_UTR	Exon 5 of 5	NP_001008541.1	P50539-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MXI1	ENST00000332674.9	TSL:1 MANE Select	c.*118_*122dupAAAAC		3_prime_UTR	Exon 6 of 6	ENSP00000331152.5	P50539-3
	MXI1	ENST00000239007.11	TSL:1	c.*118_*122dupAAAAC		3_prime_UTR	Exon 6 of 6	ENSP00000239007.7	P50539-1
	MXI1	ENST00000361248.8	TSL:1	c.*118_*122dupAAAAC		3_prime_UTR	Exon 5 of 5	ENSP00000354606.4	P50539-4

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

African (AFR) AF: 0.0000931 AC: 2 AN: 21492

American (AMR) AF: 0.0000774 AC: 1 AN: 12916

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14122

East Asian (EAS) AF: 0.000144 AC: 4 AN: 27798

South Asian (SAS) AF: 0.00185 AC: 63 AN: 34142

European-Finnish (FIN) AF: 0.00198 AC: 72 AN: 36306

Middle Eastern (MID) AF: 0.000599 AC: 2 AN: 3340

European-Non Finnish (NFE) AF: 0.000295 AC: 167 AN: 565378

Other (OTH) AF: 0.000347 AC: 12 AN: 34538

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

African (AFR) AF: 0.000121 AC: 5 AN: 41462

American (AMR) AF: 0.00 AC: 0 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3454

East Asian (EAS) AF: 0.000196 AC: 1 AN: 5098

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4820

European-Finnish (FIN) AF: 0.00336 AC: 35 AN: 10426

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000384 AC: 26 AN: 67764

Other (OTH) AF: 0.000952 AC: 2 AN: 2100

Alfa AF: 0.000184 Hom.: 895

Bravo AF: 0.000230

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16448; hg19: chr10-112044842;