12-122143882-T-C

Variant names:

• chr12-122143882-T-C
• rs3741452
• NM_014938.6:c.*2070T>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014938.6(MLXIP):​c.*2070T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: MLXIP NM_014938.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLXIP	NM_014938.6	c.*2070T>C		3_prime_UTR_variant	Exon 17 of 17	ENST00000319080.12	NP_055753.3
MLXIP	XM_006719290.5	c.*2062T>C		3_prime_UTR_variant	Exon 18 of 18		XP_006719353.1
MLXIP	XM_006719291.5	c.*2062T>C		3_prime_UTR_variant	Exon 18 of 18		XP_006719354.1
MLXIP	XM_006719292.5	c.*2070T>C		3_prime_UTR_variant	Exon 17 of 17		XP_006719355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLXIP	ENST00000319080.12	c.*2070T>C		3_prime_UTR_variant	Exon 17 of 17	1	NM_014938.6	ENSP00000312834.6
MLXIP	ENST00000538698.5	c.*2070T>C		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000440769.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	9.7
DANN	Benign	0.80
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3741452; hg19: chr12-122628429;