rs16448

Variant names:

• chr10-110285084-TAAAACAAAAC-T
• rs16448
• NM_130439.3:c.*113_*122delAAAACAAAAC

Your query was ambiguous. Multiple possible variants found:

• chr10-110285084-TAAAACAAAAC-T
• chr10-110285084-TAAAACAAAAC-TAAAAC
• chr10-110285084-TAAAACAAAAC-TAAAACAAAACAAAAC

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_130439.3(MXI1):​c.*113_*122delAAAACAAAAC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000061 in 901,546 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000099 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000053 (0 hom.)
• Consequence: MXI1 NM_130439.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.42
• 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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.*113_*122delAAAACAAAAC		3_prime_UTR	Exon 6 of 6	NP_569157.2	P50539-3
	MXI1	NM_005962.5		c.*113_*122delAAAACAAAAC		3_prime_UTR	Exon 6 of 6	NP_005953.4
	MXI1	NM_001008541.1		c.*113_*122delAAAACAAAAC		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.*113_*122delAAAACAAAAC		3_prime_UTR	Exon 6 of 6	ENSP00000331152.5	P50539-3
	MXI1	ENST00000239007.11	TSL:1	c.*113_*122delAAAACAAAAC		3_prime_UTR	Exon 6 of 6	ENSP00000239007.7	P50539-1
	MXI1	ENST00000361248.8	TSL:1	c.*113_*122delAAAACAAAAC		3_prime_UTR	Exon 5 of 5	ENSP00000354606.4	P50539-4

Frequencies

GnomAD3 genomes AF: 0.0000991 AC: 15 AN: 151422 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000132

Gnomad ASJ AF: 0.000290

Gnomad EAS AF: 0.000391

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0000959

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000533 AC: 40 AN: 750004 Hom.: 0 AF XY: 0.0000508 AC XY: 19 AN XY: 373870

African (AFR) AF: 0.00 AC: 0 AN: 21492

American (AMR) AF: 0.000155 AC: 2 AN: 12916

Ashkenazi Jewish (ASJ) AF: 0.000779 AC: 11 AN: 14118

East Asian (EAS) AF: 0.000108 AC: 3 AN: 27794

South Asian (SAS) AF: 0.00 AC: 0 AN: 34140

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36304

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3340

European-Non Finnish (NFE) AF: 0.0000389 AC: 22 AN: 565364

Other (OTH) AF: 0.0000579 AC: 2 AN: 34536

GnomAD4 genome AF: 0.0000990 AC: 15 AN: 151542 Hom.: 0 Cov.: 0 AF XY: 0.000108 AC XY: 8 AN XY: 74000

African (AFR) AF: 0.00 AC: 0 AN: 41462

American (AMR) AF: 0.000131 AC: 2 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.000290 AC: 1 AN: 3454

East Asian (EAS) AF: 0.000392 AC: 2 AN: 5098

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4820

European-Finnish (FIN) AF: 0.0000959 AC: 1 AN: 10426

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

European-Non Finnish (NFE) AF: 0.000118 AC: 8 AN: 67764

Other (OTH) AF: 0.00 AC: 0 AN: 2100

Alfa AF: 0.00 Hom.: 895

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.4

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;