dbSNP rs7270085: MAPRE1:c.*1073G>A (chr20-32849801-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_012325.3(MAPRE1):c.*1073G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 152,616 control chromosomes in the GnomAD database, including 533 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 0.058 ( 533 hom., cov: 32)

Exomes 𝑓: 0.013 ( 0 hom. )

Consequence

MAPRE1
NM_012325.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.736

Publications

15 publications found

Variant links:

Genes affected

MAPRE1 (HGNC:6890): (microtubule associated protein RP/EB family member 1) The protein encoded by this gene was first identified by its binding to the APC protein which is often mutated in familial and sporadic forms of colorectal cancer. This protein localizes to microtubules, especially the growing ends, in interphase cells. During mitosis, the protein is associated with the centrosomes and spindle microtubules. The protein also associates with components of the dynactin complex and the intermediate chain of cytoplasmic dynein. Because of these associations, it is thought that this protein is involved in the regulation of microtubule structures and chromosome stability. This gene is a member of the RP/EB family. [provided by RefSeq, Jul 2008]

MAPRE1 links:

ENSG00000260536 (HGNC:):

ENSG00000260536 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=-0.57).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAPRE1	NM_012325.3 link	c.*1073G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000375571.6	NP_036457.1	Q15691
MAPRE1	XM_011528696.3 link	c.*1073G>A		3_prime_UTR_variant	Exon 7 of 7		XP_011526998.1	Q15691

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAPRE1	ENST00000375571.6 link	c.*1073G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_012325.3	ENSP00000364721.5		Q15691
ENSG00000260536	ENST00000565572.1 link	n.80+4377C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.0580

AC:

8813

AN:

152046

Hom.:

532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0235

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0448

Gnomad FIN

AF:

0.0167

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0193

Gnomad OTH

AF:

0.0331

GnomAD4 exome

AF:

0.0133

AC:

AN:

452

Hom.:

Cov.:

AF XY:

0.0184

AC XY:

AN XY:

272

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0140

AC:

AN:

428

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0580

AC:

8827

AN:

152164

Hom.:

533

Cov.:

AF XY:

0.0574

AC XY:

4271

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.160

AC:

6644

AN:

41476

American (AMR)

AF:

0.0233

AC:

357

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00317

AC:

AN:

3470

East Asian (EAS)

AF:

0.00231

AC:

AN:

5186

South Asian (SAS)

AF:

0.0440

AC:

212

AN:

4816

European-Finnish (FIN)

AF:

0.0167

AC:

177

AN:

10604

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0193

AC:

1313

AN:

68004

Other (OTH)

AF:

0.0328

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

390

779

1169

1558

1948

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0589

Hom.:

321

Bravo

AF:

0.0616

Asia WGS

AF:

0.0460

AC:

159

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

6.5

(source)

DANN

Benign

0.85

PhyloP100

-0.74

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over