Variant rs4902359 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002382.5(MAX):c.*404C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 1,214,674 control chromosomes in the GnomAD database, including 106,086 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 20060 hom., cov: 33)

Exomes 𝑓: 0.40 ( 86026 hom. )

Consequence

MAX
NM_002382.5 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.41

Variant links:

Genes affected

MAX (HGNC:6913): (MYC associated factor X) The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Mutations of this gene have been reported to be associated with hereditary pheochromocytoma. A pseudogene of this gene is located on the long arm of chromosome 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

MAX links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 14-65076072-G-A is Benign according to our data. Variant chr14-65076072-G-A is described in ClinVar as [Benign]. Clinvar id is 313807.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAX	NM_002382.5 linkuse as main transcript	c.*404C>T		3_prime_UTR_variant	5/5	ENST00000358664.9	NP_002373.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAX	ENST00000358664.9 linkuse as main transcript	c.*404C>T		3_prime_UTR_variant	5/5	1	NM_002382.5	ENSP00000351490	P4	P61244-1

Frequencies

GnomAD3 genomes

AF:

0.479

AC:

72840

AN:

151990

Hom.:

20026

Cov.:

show subpopulations

Gnomad AFR

AF:

0.768

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.422

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.368

Gnomad OTH

AF:

0.426

GnomAD4 exome

AF:

0.395

AC:

419880

AN:

1062568

Hom.:

86026

Cov.:

AF XY:

0.395

AC XY:

198221

AN XY:

501542

show subpopulations

Gnomad4 AFR exome

AF:

0.793

Gnomad4 AMR exome

AF:

0.264

Gnomad4 ASJ exome

AF:

0.289

Gnomad4 EAS exome

AF:

0.472

Gnomad4 SAS exome

AF:

0.477

Gnomad4 FIN exome

AF:

0.402

Gnomad4 NFE exome

AF:

0.382

Gnomad4 OTH exome

AF:

0.408

GnomAD4 genome

AF:

0.479

AC:

72919

AN:

152106

Hom.:

20060

Cov.:

AF XY:

0.478

AC XY:

35503

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.768

Gnomad4 AMR

AF:

0.306

Gnomad4 ASJ

AF:

0.287

Gnomad4 EAS

AF:

0.418

Gnomad4 SAS

AF:

0.495

Gnomad4 FIN

AF:

0.422

Gnomad4 NFE

AF:

0.368

Gnomad4 OTH

AF:

0.423

Alfa

AF:

0.375

Hom.:

18236

Bravo

AF:

0.479

Asia WGS

AF:

0.466

AC:

1618

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Pheochromocytoma

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.1

DANN

Benign

0.69

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

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