GeneBe

ENST00000569515.1:n.281+13891A>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000569515.1(MCMBP):​n.281+13891A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,024 control chromosomes in the GnomAD database, including 22,743 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 0.54 ( 22743 hom., cov: 32)

Consequence

MCMBP
ENST00000569515.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.160

Publications

9 publications found
Variant links:
Genes affected
MCMBP (HGNC:25782): (minichromosome maintenance complex binding protein) This gene encodes a protein which is a component of the hexameric minichromosome maintenance (MCM) complex which regulates initiation and elongation of DNA. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MCMBPENST00000569515.1 linkn.281+13891A>G intron_variant Intron 2 of 3 5

Frequencies

GnomAD3 genomes
AF:
0.542
AC:
82330
AN:
151906
Hom.:
22721
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.623
Gnomad AMI
AF:
0.425
Gnomad AMR
AF:
0.584
Gnomad ASJ
AF:
0.523
Gnomad EAS
AF:
0.625
Gnomad SAS
AF:
0.292
Gnomad FIN
AF:
0.562
Gnomad MID
AF:
0.487
Gnomad NFE
AF:
0.494
Gnomad OTH
AF:
0.545
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.542
AC:
82398
AN:
152024
Hom.:
22743
Cov.:
32
AF XY:
0.543
AC XY:
40350
AN XY:
74296
show subpopulations
African (AFR)
AF:
0.622
AC:
25797
AN:
41460
American (AMR)
AF:
0.585
AC:
8936
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.523
AC:
1813
AN:
3468
East Asian (EAS)
AF:
0.624
AC:
3227
AN:
5170
South Asian (SAS)
AF:
0.292
AC:
1408
AN:
4820
European-Finnish (FIN)
AF:
0.562
AC:
5935
AN:
10556
Middle Eastern (MID)
AF:
0.483
AC:
141
AN:
292
European-Non Finnish (NFE)
AF:
0.494
AC:
33601
AN:
67954
Other (OTH)
AF:
0.545
AC:
1152
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1953
3905
5858
7810
9763
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
706
1412
2118
2824
3530
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.507
Hom.:
24340
Bravo
AF:
0.552
Asia WGS
AF:
0.470
AC:
1638
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.8
DANN
Benign
0.55
PhyloP100
-0.16

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2939931; hg19: chr10-121636406; API