Variant chr17-4555186-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_014520.4(MYBBP1A):c.139C>G(p.Gln47Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000000687 in 1,455,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

MYBBP1A
NM_014520.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.63

Variant links:

Genes affected

MYBBP1A (HGNC:7546): (MYB binding protein 1a) This gene encodes a nucleolar transcriptional regulator that was first identified by its ability to bind specifically to the Myb proto-oncogene protein. The encoded protein is thought to play a role in many cellular processes including response to nucleolar stress, tumor suppression and synthesis of ribosomal DNA. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

MYBBP1A links:

MYBBP1A (HGNC:):

MYBBP1A links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.33204496).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYBBP1A	NM_014520.4 linkuse as main transcript	c.139C>G	p.Gln47Glu	missense_variant	1/26	ENST00000254718.9	NP_055335.2	Q9BQG0-1
MYBBP1A	NM_001105538.2 linkuse as main transcript	c.139C>G	p.Gln47Glu	missense_variant	1/27		NP_001099008.1	Q9BQG0-2
MYBBP1A	XM_024450536.2 linkuse as main transcript	c.139C>G	p.Gln47Glu	missense_variant	1/25		XP_024306304.1
MYBBP1A	XM_047435119.1 linkuse as main transcript	c.139C>G	p.Gln47Glu	missense_variant	1/17		XP_047291075.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MYBBP1A	ENST00000254718.9 linkuse as main transcript	c.139C>G	p.Gln47Glu	missense_variant	1/26	1	NM_014520.4	ENSP00000254718.4	Q9BQG0-1
MYBBP1A	ENST00000381556.6 linkuse as main transcript	c.139C>G	p.Gln47Glu	missense_variant	1/27	5		ENSP00000370968.2	Q9BQG0-2
MYBBP1A	ENST00000570986.1 linkuse as main transcript	n.173C>G		non_coding_transcript_exon_variant	1/6	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000420

AC:

AN:

238074

Hom.:

AF XY:

0.00000772

AC XY:

AN XY:

129536

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000561

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

6.87e-7

AC:

AN:

1455586

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

723642

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.096

BayesDel_addAF

Benign

-0.13

BayesDel_noAF

Benign

-0.24

CADD

Uncertain

DANN

Uncertain

0.98

DEOGEN2

Benign

0.034

.;T

Eigen

Benign

0.13

Eigen_PC

Uncertain

0.23

FATHMM_MKL

Uncertain

0.96

LIST_S2

Uncertain

0.89

D;D

M_CAP

Benign

0.038

MetaRNN

Benign

0.33

T;T

MetaSVM

Benign

-0.74

MutationAssessor

Benign

1.8

L;L

MutationTaster

Benign

0.54

D;D

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-0.80

N;N

REVEL

Benign

0.14

Sift

Benign

0.30

T;T

Sift4G

Uncertain

0.012

D;D

Polyphen

0.80

P;P

Vest4

0.43

MutPred

0.34

Gain of disorder (P = 0.0655);Gain of disorder (P = 0.0655);

MVP

0.83

ClinPred

0.45

GERP RS

4.8

Varity_R

0.27

gMVP

0.17

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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