Menu
GeneBe

17-4539910-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_014520.4(MYBBP1A):c.3492C>T(p.Pro1164=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000835 in 1,600,358 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 5 hom., cov: 31)
Exomes 𝑓: 0.00046 ( 3 hom. )

Consequence

MYBBP1A
NM_014520.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.51
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 17-4539910-G-A is Benign according to our data. Variant chr17-4539910-G-A is described in ClinVar as [Benign]. Clinvar id is 709927.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.51 with no splicing effect.
BS2
High AC in GnomAd at 663 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYBBP1ANM_014520.4 linkuse as main transcriptc.3492C>T p.Pro1164= synonymous_variant 26/26 ENST00000254718.9
MYBBP1AXM_024450536.2 linkuse as main transcriptc.3355C>T p.His1119Tyr missense_variant 25/25
MYBBP1ANM_001105538.2 linkuse as main transcriptc.3492C>T p.Pro1164= synonymous_variant 26/27
MYBBP1AXM_011523616.3 linkuse as main transcriptc.2736C>T p.Pro912= synonymous_variant 21/21

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYBBP1AENST00000254718.9 linkuse as main transcriptc.3492C>T p.Pro1164= synonymous_variant 26/261 NM_014520.4 P2Q9BQG0-1

Frequencies

GnomAD3 genomes
AF:
0.00436
AC:
663
AN:
152092
Hom.:
5
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0150
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00151
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000882
Gnomad OTH
AF:
0.00478
GnomAD3 exomes
AF:
0.00118
AC:
283
AN:
240670
Hom.:
5
AF XY:
0.000839
AC XY:
110
AN XY:
131090
show subpopulations
Gnomad AFR exome
AF:
0.0154
Gnomad AMR exome
AF:
0.00101
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000663
GnomAD4 exome
AF:
0.000465
AC:
673
AN:
1448148
Hom.:
3
Cov.:
36
AF XY:
0.000415
AC XY:
299
AN XY:
720812
show subpopulations
Gnomad4 AFR exome
AF:
0.0161
Gnomad4 AMR exome
AF:
0.00121
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000927
Gnomad4 FIN exome
AF:
0.0000251
Gnomad4 NFE exome
AF:
0.00000540
Gnomad4 OTH exome
AF:
0.00101
GnomAD4 genome
AF:
0.00436
AC:
663
AN:
152210
Hom.:
5
Cov.:
31
AF XY:
0.00399
AC XY:
297
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.0150
Gnomad4 AMR
AF:
0.00150
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000882
Gnomad4 OTH
AF:
0.00473
Alfa
AF:
0.00184
Hom.:
0
Bravo
AF:
0.00487
Asia WGS
AF:
0.00173
AC:
6
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 28, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
0.10
Dann
Benign
0.60
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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.

Other links and lift over

dbSNP: rs76804207; hg19: chr17-4443205; API