Variant 17-2388029-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_020310.3(MNT):c.828G>A(p.Lys276=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0026 in 1,561,188 control chromosomes in the GnomAD database, including 118 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0052 ( 24 hom., cov: 33)

Exomes 𝑓: 0.0023 ( 94 hom. )

Consequence

MNT
NM_020310.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0330

Variant links:

Genes affected

MNT (HGNC:7188): (MAX network transcriptional repressor) The Myc/Max/Mad network comprises a group of transcription factors that co-interact to regulate gene-specific transcriptional activation or repression. This gene encodes a protein member of the Myc/Max/Mad network. This protein has a basic-Helix-Loop-Helix-zipper domain (bHLHzip) with which it binds the canonical DNA sequence CANNTG, known as the E box, following heterodimerization with Max proteins. This protein is likely a transcriptional repressor and an antagonist of Myc-dependent transcriptional activation and cell growth. This protein represses transcription by binding to DNA binding proteins at its N-terminal Sin3-interaction domain. [provided by RefSeq, Jul 2008]

MNT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001423955).

BP6

Variant 17-2388029-C-T is Benign according to our data. Variant chr17-2388029-C-T is described in ClinVar as [Benign]. Clinvar id is 770261.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.033 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MNT	NM_020310.3 linkuse as main transcript	c.828G>A	p.Lys276=	synonymous_variant	5/6	ENST00000174618.5	NP_064706.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MNT	ENST00000174618.5 linkuse as main transcript	c.828G>A	p.Lys276=	synonymous_variant	5/6	1	NM_020310.3	ENSP00000174618	P1

Frequencies

GnomAD3 genomes

AF:

0.00516

AC:

786

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000555

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0398

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0133

Gnomad SAS

AF:

0.00165

Gnomad FIN

AF:

0.000847

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000809

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.0106

AC:

1806

AN:

169590

Hom.:

AF XY:

0.00871

AC XY:

781

AN XY:

89682

show subpopulations

Gnomad AFR exome

AF:

0.000201

Gnomad AMR exome

AF:

0.0584

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0105

Gnomad SAS exome

AF:

0.00192

Gnomad FIN exome

AF:

0.000565

Gnomad NFE exome

AF:

0.000725

Gnomad OTH exome

AF:

0.00768

GnomAD4 exome

AF:

0.00232

AC:

3262

AN:

1408862

Hom.:

Cov.:

AF XY:

0.00219

AC XY:

1524

AN XY:

696108

show subpopulations

Gnomad4 AFR exome

AF:

0.000469

Gnomad4 AMR exome

AF:

0.0561

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0108

Gnomad4 SAS exome

AF:

0.00171

Gnomad4 FIN exome

AF:

0.000662

Gnomad4 NFE exome

AF:

0.000390

Gnomad4 OTH exome

AF:

0.00276

GnomAD4 genome

AF:

0.00519

AC:

790

AN:

152326

Hom.:

Cov.:

AF XY:

0.00613

AC XY:

457

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.000553

Gnomad4 AMR

AF:

0.0400

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0133

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.000847

Gnomad4 NFE

AF:

0.000809

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.000728

Hom.:

Bravo

AF:

0.00847

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.000815

AC:

ExAC

AF:

0.00521

AC:

607

Asia WGS

AF:

0.00895

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jun 19, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.60

CADD

Benign

1.5

DANN

Benign

0.66

DEOGEN2

Benign

0.0062

FATHMM_MKL

Benign

0.63

LIST_S2

Benign

0.45

MetaRNN

Benign

0.0014

MutationTaster

Benign

1.0

D;D

Vest4

0.20

GERP RS

0.93

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over