dbSNP rs1043763: MLXIP:c.*4550G>A (chr12-122146362-G-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.*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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.298

Publications

4 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
MLXIP	NM_014938.6 link	c.*4550G>A	3_prime_UTR_variant	Exon 17 of 17	ENST00000319080.12	NP_055753.3
MLXIP	XM_006719290.5 link	c.*4542G>A	3_prime_UTR_variant	Exon 18 of 18		XP_006719353.1
MLXIP	XM_006719291.5 link	c.*4542G>A	3_prime_UTR_variant	Exon 18 of 18		XP_006719354.1
MLXIP	XM_006719292.5 link	c.*4550G>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 link	c.*4550G>A		3_prime_UTR_variant	Exon 17 of 17	1	NM_014938.6	ENSP00000312834.6

Frequencies

GnomAD3 genomes

AF:

0.716

AC:

108276

AN:

151290

Hom.:

39485

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.721

AC XY:

101

AN XY:

140

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.778

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.725

AC:

AN:

120

Other (OTH)

AF:

0.563

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.716

AC:

108347

AN:

151408

Hom.:

39504

Cov.:

AF XY:

0.714

AC XY:

52823

AN XY:

73950

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1492

2984

4475

5967

7459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

826

1652

2478

3304

4130

<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:

0.769

Hom.:

120317

Bravo

AF:

0.712

Asia WGS

AF:

0.639

AC:

2223

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.7

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over