Variant rs2070583 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000621592.8(MYC):c.*50A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0291 in 1,473,676 control chromosomes in the GnomAD database, including 1,226 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 0.031 ( 165 hom., cov: 32)

Exomes 𝑓: 0.029 ( 1061 hom. )

Consequence

MYC
ENST00000621592.8 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.681

Variant links:

Genes affected

MYC (HGNC:7553): (MYC proto-oncogene, bHLH transcription factor) This gene is a proto-oncogene and encodes a nuclear phosphoprotein that plays a role in cell cycle progression, apoptosis and cellular transformation. The encoded protein forms a heterodimer with the related transcription factor MAX. This complex binds to the E box DNA consensus sequence and regulates the transcription of specific target genes. Amplification of this gene is frequently observed in numerous human cancers. Translocations involving this gene are associated with Burkitt lymphoma and multiple myeloma in human patients. There is evidence to show that translation initiates both from an upstream, in-frame non-AUG (CUG) and a downstream AUG start site, resulting in the production of two isoforms with distinct N-termini. [provided by RefSeq, Aug 2017]

MYC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYC	NM_002467.6 linkuse as main transcript	c.*50A>G		3_prime_UTR_variant	3/3	ENST00000621592.8	NP_002458.2
MYC	NM_001354870.1 linkuse as main transcript	c.*50A>G		3_prime_UTR_variant	3/3		NP_001341799.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYC	ENST00000621592.8 linkuse as main transcript	c.*50A>G		3_prime_UTR_variant	3/3	1	NM_002467.6	ENSP00000478887	A2	P01106-2

Frequencies

GnomAD3 genomes

AF:

0.0313

AC:

4761

AN:

152150

Hom.:

163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0199

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0707

Gnomad ASJ

AF:

0.0251

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.0869

Gnomad FIN

AF:

0.00895

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0209

Gnomad OTH

AF:

0.0224

GnomAD3 exomes

AF:

0.0416

AC:

6559

AN:

157744

Hom.:

284

AF XY:

0.0422

AC XY:

3553

AN XY:

84232

show subpopulations

Gnomad AFR exome

AF:

0.0200

Gnomad AMR exome

AF:

0.0450

Gnomad ASJ exome

AF:

0.0212

Gnomad EAS exome

AF:

0.151

Gnomad SAS exome

AF:

0.0957

Gnomad FIN exome

AF:

0.0129

Gnomad NFE exome

AF:

0.0194

Gnomad OTH exome

AF:

0.0312

GnomAD4 exome

AF:

0.0289

AC:

38141

AN:

1321406

Hom.:

1061

Cov.:

AF XY:

0.0303

AC XY:

19620

AN XY:

646850

show subpopulations

Gnomad4 AFR exome

AF:

0.0189

Gnomad4 AMR exome

AF:

0.0442

Gnomad4 ASJ exome

AF:

0.0198

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.0893

Gnomad4 FIN exome

AF:

0.0121

Gnomad4 NFE exome

AF:

0.0215

Gnomad4 OTH exome

AF:

0.0305

GnomAD4 genome

AF:

0.0313

AC:

4765

AN:

152270

Hom.:

165

Cov.:

AF XY:

0.0344

AC XY:

2563

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.0198

Gnomad4 AMR

AF:

0.0710

Gnomad4 ASJ

AF:

0.0251

Gnomad4 EAS

AF:

0.148

Gnomad4 SAS

AF:

0.0869

Gnomad4 FIN

AF:

0.00895

Gnomad4 NFE

AF:

0.0209

Gnomad4 OTH

AF:

0.0217

Alfa

AF:

0.0233

Hom.:

Bravo

AF:

0.0318

Asia WGS

AF:

0.0960

AC:

335

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.6

DANN

Benign

0.58

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over