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GeneBe

8-120453883-G-A

Variant summary

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

The NM_022045.5(MTBP):c.462G>A(p.Leu154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000278 in 1,579,926 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0014 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00016 ( 2 hom. )

Consequence

MTBP
NM_022045.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00900
Variant links:
Genes affected
MTBP (HGNC:7417): (MDM2 binding protein) This gene encodes a protein that interacts with the oncoprotein mouse double minute 2. The encoded protein regulates progression through the cell cycle and may be involved in tumor formation. [provided by RefSeq, Aug 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 8-120453883-G-A is Benign according to our data. Variant chr8-120453883-G-A is described in ClinVar as [Benign]. Clinvar id is 724478.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.009 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MTBPNM_022045.5 linkuse as main transcriptc.462G>A p.Leu154= synonymous_variant 5/22 ENST00000305949.6
MTBPXM_011516962.3 linkuse as main transcriptc.462G>A p.Leu154= synonymous_variant 5/18
MTBPXM_011516963.3 linkuse as main transcriptc.462G>A p.Leu154= synonymous_variant 5/14
MTBPXR_928318.3 linkuse as main transcriptn.514G>A non_coding_transcript_exon_variant 5/19

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MTBPENST00000305949.6 linkuse as main transcriptc.462G>A p.Leu154= synonymous_variant 5/221 NM_022045.5 P1Q96DY7-1
MTBPENST00000523373.5 linkuse as main transcriptc.462G>A p.Leu154= synonymous_variant, NMD_transcript_variant 5/115 Q96DY7-3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00143
AC:
217
AN:
152064
Hom.:
3
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00493
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000411
AC:
98
AN:
238270
Hom.:
3
AF XY:
0.000348
AC XY:
45
AN XY:
129188
show subpopulations
Gnomad AFR exome
AF:
0.00544
Gnomad AMR exome
AF:
0.000127
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000588
Gnomad SAS exome
AF:
0.0000353
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000641
Gnomad OTH exome
AF:
0.000177
GnomAD4 exome
AF:
0.000156
AC:
223
AN:
1427744
Hom.:
2
Cov.:
26
AF XY:
0.000137
AC XY:
97
AN XY:
710368
show subpopulations
Gnomad4 AFR exome
AF:
0.00495
Gnomad4 AMR exome
AF:
0.000142
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000523
Gnomad4 SAS exome
AF:
0.0000372
Gnomad4 FIN exome
AF:
0.0000190
Gnomad4 NFE exome
AF:
0.0000302
Gnomad4 OTH exome
AF:
0.000273
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00143
AC:
217
AN:
152182
Hom.:
3
Cov.:
32
AF XY:
0.00141
AC XY:
105
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.00491
Gnomad4 AMR
AF:
0.000458
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.000365
Hom.:
0
Bravo
AF:
0.00171
Asia WGS
AF:
0.000579
AC:
2
AN:
3468

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 testingInvitaeAug 20, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
Cadd
Benign
5.5
Dann
Benign
0.69
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: rs147445942; hg19: chr8-121466123; API