Genetic Variant MON1B:c.475+210C>G (chr16-77193987-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_014940.4(MON1B):c.475+210C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 611,402 control chromosomes in the GnomAD database, including 136,186 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 0.69 ( 37739 hom., cov: 31)

Exomes 𝑓: 0.65 ( 98447 hom. )

Consequence

MON1B
NM_014940.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.71

Publications

8 publications found

Variant links:

Genes affected

MON1B (HGNC:25020): (MON1 homolog B, secretory trafficking associated) Involved in early viral transcription and late viral transcription. Located in cytoplasm. Part of Mon1-Ccz1 complex. [provided by Alliance of Genome Resources, Apr 2022]

MON1B links:

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014940.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MON1B	NM_014940.4	MANE Select	c.475+210C>G	intron	N/A	NP_055755.1
MON1B	NM_001286639.2		c.149-348C>G	intron	N/A	NP_001273568.1
MON1B	NM_001286640.2		c.38-348C>G	intron	N/A	NP_001273569.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MON1B	ENST00000248248.8	TSL:1 MANE Select	c.475+210C>G	intron	N/A	ENSP00000248248.3
MON1B	ENST00000566455.1	TSL:2	n.20C>G	non_coding_transcript_exon	Exon 1 of 3
MON1B	ENST00000439557.6	TSL:2	c.149-348C>G	intron	N/A	ENSP00000404053.2

Frequencies

GnomAD3 genomes

AF:

0.695

AC:

105418

AN:

151758

Hom.:

37694

Cov.:

show subpopulations

Gnomad AFR

AF:

0.855

Gnomad AMI

AF:

0.582

Gnomad AMR

AF:

0.728

Gnomad ASJ

AF:

0.614

Gnomad EAS

AF:

0.854

Gnomad SAS

AF:

0.717

Gnomad FIN

AF:

0.544

Gnomad MID

AF:

0.769

Gnomad NFE

AF:

0.605

Gnomad OTH

AF:

0.691

GnomAD4 exome

AF:

0.648

AC:

297887

AN:

459526

Hom.:

98447

Cov.:

AF XY:

0.652

AC XY:

157055

AN XY:

241032

show subpopulations

African (AFR)

AF:

0.858

AC:

10856

AN:

12652

American (AMR)

AF:

0.747

AC:

13577

AN:

18166

Ashkenazi Jewish (ASJ)

AF:

0.621

AC:

8540

AN:

13746

East Asian (EAS)

AF:

0.850

AC:

26422

AN:

31078

South Asian (SAS)

AF:

0.728

AC:

33107

AN:

45478

European-Finnish (FIN)

AF:

0.561

AC:

16804

AN:

29944

Middle Eastern (MID)

AF:

0.732

AC:

1463

AN:

1998

European-Non Finnish (NFE)

AF:

0.607

AC:

169954

AN:

280208

Other (OTH)

AF:

0.654

AC:

17164

AN:

26256

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

5260

10519

15779

21038

26298

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1052

2104

3156

4208

5260

<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:

0.695

AC:

105522

AN:

151876

Hom.:

37739

Cov.:

AF XY:

0.695

AC XY:

51552

AN XY:

74192

show subpopulations

African (AFR)

AF:

0.855

AC:

35391

AN:

41406

American (AMR)

AF:

0.728

AC:

11123

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.614

AC:

2128

AN:

3464

East Asian (EAS)

AF:

0.853

AC:

4368

AN:

5118

South Asian (SAS)

AF:

0.716

AC:

3451

AN:

4820

European-Finnish (FIN)

AF:

0.544

AC:

5741

AN:

10546

Middle Eastern (MID)

AF:

0.776

AC:

228

AN:

294

European-Non Finnish (NFE)

AF:

0.605

AC:

41097

AN:

67928

Other (OTH)

AF:

0.695

AC:

1465

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1522

3044

4565

6087

7609

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

816

1632

2448

3264

4080

<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:

0.658

Hom.:

4199

Bravo

AF:

0.712

Asia WGS

AF:

0.826

AC:

2869

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.0030

(source)

DANN

Benign

0.64

PhyloP100

-2.7

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over