rs7953704

Variant names:

• chr12-122141445-A-G
• rs7953704
• NM_014938.6:c.2639-246A>G

Variant summary

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

The NM_014938.6(MLXIP):​c.2639-246A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,084 control chromosomes in the GnomAD database, including 23,745 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 0.56 (23745 hom., cov: 32)
• Consequence: MLXIP NM_014938.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 29 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 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.2639-246A>G		intron	N/A	NP_055753.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLXIP	ENST00000319080.12	TSL:1 MANE Select	c.2639-246A>G		intron	N/A	ENSP00000312834.6	Q9HAP2-1
	MLXIP	ENST00000538698.5	TSL:1	c.1460-246A>G		intron	N/A	ENSP00000440769.1	Q9HAP2-2
	MLXIP	ENST00000890512.1		c.2642-246A>G		intron	N/A	ENSP00000560571.1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84444 AN: 151966 Hom.: 23732 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.538

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.556 AC: 84504 AN: 152084 Hom.: 23745 Cov.: 32 AF XY: 0.557 AC XY: 41384 AN XY: 74338

African (AFR) AF: 0.601 AC: 24948 AN: 41478

American (AMR) AF: 0.595 AC: 9096 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3466

East Asian (EAS) AF: 0.511 AC: 2638 AN: 5158

South Asian (SAS) AF: 0.518 AC: 2498 AN: 4820

European-Finnish (FIN) AF: 0.597 AC: 6324 AN: 10594

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36007 AN: 67962

Other (OTH) AF: 0.536 AC: 1134 AN: 2114

Alfa AF: 0.542 Hom.: 34673

Bravo AF: 0.556

Asia WGS AF: 0.527 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.49
PhyloP100		-2.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs7953704; hg19: chr12-122625992;