Variant chr14-65075759-A-G 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.*717T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 1,065,706 control chromosomes in the GnomAD database, including 60,500 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6157 hom., cov: 32)

Exomes 𝑓: 0.34 ( 54343 hom. )

Consequence

MAX
NM_002382.5 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.58

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 14-65075759-A-G is Benign according to our data. Variant chr14-65075759-A-G is described in ClinVar as [Benign]. Clinvar id is 313798.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAX	NM_002382.5 linkuse as main transcript	c.*717T>C		3_prime_UTR_variant	5/5	ENST00000358664.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAX	ENST00000358664.9 linkuse as main transcript	c.*717T>C		3_prime_UTR_variant	5/5	1	NM_002382.5	P4	P61244-1

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

41081

AN:

151906

Hom.:

6161

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.220

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.280

Gnomad FIN

AF:

0.397

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.339

Gnomad OTH

AF:

0.242

GnomAD4 exome

AF:

0.342

AC:

312501

AN:

913682

Hom.:

54343

Cov.:

AF XY:

0.343

AC XY:

144495

AN XY:

421856

show subpopulations

Gnomad4 AFR exome

AF:

0.149

Gnomad4 AMR exome

AF:

0.180

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.212

Gnomad4 SAS exome

AF:

0.278

Gnomad4 FIN exome

AF:

0.365

Gnomad4 NFE exome

AF:

0.354

Gnomad4 OTH exome

AF:

0.311

GnomAD4 genome

AF:

0.270

AC:

41082

AN:

152024

Hom.:

6157

Cov.:

AF XY:

0.271

AC XY:

20113

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.166

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.220

Gnomad4 EAS

AF:

0.144

Gnomad4 SAS

AF:

0.280

Gnomad4 FIN

AF:

0.397

Gnomad4 NFE

AF:

0.339

Gnomad4 OTH

AF:

0.239

Alfa

AF:

0.309

Hom.:

7580

Bravo

AF:

0.249

Asia WGS

AF:

0.200

AC:

695

AN:

3478

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

-0.92

CADD

Benign

0.22

DANN

Benign

0.47

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

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