Genetic Variant MCMBP:c.1796+13C>T (chr10-119831999-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001256378.2(MCMBP):c.1796+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,602,792 control chromosomes in the GnomAD database, including 30,832 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 0.17 ( 2288 hom., cov: 32)

Exomes 𝑓: 0.19 ( 28544 hom. )

Consequence

MCMBP
NM_001256378.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.724

Publications

17 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]

MCMBP links:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCMBP	NM_001256378.2 link	c.1796+13C>T		intron_variant	Intron 15 of 15	ENST00000369077.4	NP_001243307.1	Q9BTE3-2A0A0S2Z5P5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MCMBP	ENST00000369077.4 link	c.1796+13C>T	intron_variant	Intron 15 of 15	1	NM_001256378.2	ENSP00000358073.3	Q9BTE3-2
MCMBP	ENST00000360003.7 link	c.1802+13C>T	intron_variant	Intron 15 of 15	2		ENSP00000353098.3	Q9BTE3-1
MCMBP	ENST00000466047.5 link	n.1898+13C>T	intron_variant	Intron 15 of 15	2

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25366

AN:

151990

Hom.:

2284

Cov.:

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.440

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.149

GnomAD2 exomes

AF:

0.196

AC:

47653

AN:

243352

AF XY:

0.210

show subpopulations

Gnomad AFR exome

AF:

0.142

Gnomad AMR exome

AF:

0.120

Gnomad ASJ exome

AF:

0.196

Gnomad EAS exome

AF:

0.185

Gnomad FIN exome

AF:

0.154

Gnomad NFE exome

AF:

0.173

Gnomad OTH exome

AF:

0.187

GnomAD4 exome

AF:

0.187

AC:

271047

AN:

1450684

Hom.:

28544

Cov.:

AF XY:

0.195

AC XY:

140835

AN XY:

721490

show subpopulations

African (AFR)

AF:

0.138

AC:

4535

AN:

32954

American (AMR)

AF:

0.121

AC:

5118

AN:

42376

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

4818

AN:

25702

East Asian (EAS)

AF:

0.182

AC:

7164

AN:

39422

South Asian (SAS)

AF:

0.432

AC:

36521

AN:

84578

European-Finnish (FIN)

AF:

0.153

AC:

8147

AN:

53226

Middle Eastern (MID)

AF:

0.210

AC:

1199

AN:

5700

European-Non Finnish (NFE)

AF:

0.173

AC:

191836

AN:

1106874

Other (OTH)

AF:

0.196

AC:

11709

AN:

59852

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

9803

19607

29410

39214

49017

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6846

13692

20538

27384

34230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.167

AC:

25382

AN:

152108

Hom.:

2288

Cov.:

AF XY:

0.170

AC XY:

12669

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.142

AC:

5901

AN:

41466

American (AMR)

AF:

0.132

AC:

2025

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.190

AC:

659

AN:

3470

East Asian (EAS)

AF:

0.180

AC:

933

AN:

5178

South Asian (SAS)

AF:

0.441

AC:

2122

AN:

4816

European-Finnish (FIN)

AF:

0.151

AC:

1599

AN:

10562

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11650

AN:

68000

Other (OTH)

AF:

0.149

AC:

315

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1072

2144

3216

4288

5360

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<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:

0.186

Hom.:

1680

Bravo

AF:

0.157

Asia WGS

AF:

0.269

AC:

938

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.045

(source)

DANN

Benign

0.58

PhyloP100

-0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over