rs3741452

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-122143882-T-A
• chr12-122143882-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014938.6(MLXIP):​c.*2070T>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 0.164 in 152,572 control chromosomes in the GnomAD database, including 2,506 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 0.16 (2485 hom., cov: 33)
  • Exomes 𝑓: 0.33 (21 hom.)
• 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLXIP	NM_014938.6	c.*2070T>A		3_prime_UTR_variant	Exon 17 of 17	ENST00000319080.12	NP_055753.3
MLXIP	XM_006719290.5	c.*2062T>A		3_prime_UTR_variant	Exon 18 of 18		XP_006719353.1
MLXIP	XM_006719291.5	c.*2062T>A		3_prime_UTR_variant	Exon 18 of 18		XP_006719354.1
MLXIP	XM_006719292.5	c.*2070T>A		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>A		3_prime_UTR_variant	Exon 17 of 17	1	NM_014938.6	ENSP00000312834.6
MLXIP	ENST00000538698.5	c.*2070T>A		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000440769.1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24826 AN: 152068 Hom.: 2484 Cov.: 33

Gnomad AFR AF: 0.0599

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.164

GnomAD4 exome AF: 0.326 AC: 126 AN: 386 Hom.: 21 Cov.: 0 AF XY: 0.319 AC XY: 72 AN XY: 226

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.348

Gnomad4 NFE exome AF: 0.156

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.163 AC: 24845 AN: 152186 Hom.: 2485 Cov.: 33 AF XY: 0.167 AC XY: 12408 AN XY: 74392

Gnomad4 AFR AF: 0.0597

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.166

Alfa AF: 0.123 Hom.: 256

Bravo AF: 0.148

Asia WGS AF: 0.231 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	9.3
DANN	Benign	0.86
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;