dbSNP rs3741452: MLXIP:c.*2070T>A (chr12-122143882-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0280

Publications

7 publications found

Variant links:

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]

MLXIP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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.*2070T>A		3_prime_UTR	Exon 17 of 17	NP_055753.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MLXIP	ENST00000319080.12	TSL:1 MANE Select	c.*2070T>A	3_prime_UTR	Exon 17 of 17	ENSP00000312834.6
MLXIP	ENST00000538698.5	TSL:1	c.*2070T>A	3_prime_UTR	Exon 9 of 9	ENSP00000440769.1
MLXIP	ENST00000890512.1		c.*2070T>A	3_prime_UTR	Exon 17 of 17	ENSP00000560571.1

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24826

AN:

152068

Hom.:

2484

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.319

AC XY:

AN XY:

226

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.348

AC:

119

AN:

342

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.156

AC:

AN:

Other (OTH)

AF:

0.100

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.163

AC:

24845

AN:

152186

Hom.:

2485

Cov.:

AF XY:

0.167

AC XY:

12408

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.0597

AC:

2478

AN:

41540

American (AMR)

AF:

0.165

AC:

2529

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0818

AC:

284

AN:

3470

East Asian (EAS)

AF:

0.262

AC:

1351

AN:

5162

South Asian (SAS)

AF:

0.222

AC:

1072

AN:

4818

European-Finnish (FIN)

AF:

0.288

AC:

3056

AN:

10600

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.199

AC:

13499

AN:

68004

Other (OTH)

AF:

0.166

AC:

349

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1054

2109

3163

4218

5272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

276

552

828

1104

1380

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

9.3

(source)

DANN

Benign

0.86

PhyloP100

0.028

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over