rs1043763

Variant names:

• chr12-122146362-G-A
• rs1043763
• NM_014938.6:c.*4550G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-122146362-G-A
• chr12-122146362-G-C
• chr12-122146362-G-T

Variant summary

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

The NM_014938.6(MLXIP):​c.*4550G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 151,606 control chromosomes in the GnomAD database, including 39,557 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 0.72 (39504 hom., cov: 30)
  • Exomes 𝑓: 0.73 (53 hom.)
• Consequence: MLXIP NM_014938.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 4 publications found

Genes affected

MLXIP (HGNC:17055): (MLX interacting protein) This gene encodes a protein that functions as part of a heterodimer to activate transcription. The encoded protein forms a heterodimer with Max-like protein X (MLX) and is involved in the regulation of genes in response to cellular glucose levels. [provided by RefSeq, Mar 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014938.6. 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
	MLXIP	NM_014938.6	MANE Select	c.*4550G>A		3_prime_UTR	Exon 17 of 17	NP_055753.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLXIP	ENST00000319080.12	TSL:1 MANE Select	c.*4550G>A		3_prime_UTR	Exon 17 of 17	ENSP00000312834.6	Q9HAP2-1

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108276 AN: 151290 Hom.: 39485 Cov.: 30

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.739

GnomAD4 exome AF: 0.732 AC: 145 AN: 198 Hom.: 53 Cov.: 0 AF XY: 0.721 AC XY: 101 AN XY: 140

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.778 AC: 42 AN: 54

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.725 AC: 87 AN: 120

Other (OTH) AF: 0.563 AC: 9 AN: 16

GnomAD4 genome AF: 0.716 AC: 108347 AN: 151408 Hom.: 39504 Cov.: 30 AF XY: 0.714 AC XY: 52823 AN XY: 73950

African (AFR) AF: 0.573 AC: 23653 AN: 41252

American (AMR) AF: 0.754 AC: 11483 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3190 AN: 3466

East Asian (EAS) AF: 0.580 AC: 2959 AN: 5102

South Asian (SAS) AF: 0.761 AC: 3660 AN: 4812

European-Finnish (FIN) AF: 0.702 AC: 7361 AN: 10488

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53538 AN: 67762

Other (OTH) AF: 0.738 AC: 1551 AN: 2102

Alfa AF: 0.769 Hom.: 120317

Bravo AF: 0.712

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.7
DANN	Benign	0.82
PhyloP100		0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1043763; hg19: chr12-122630909;