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GeneBe

rs2235760

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012325.3(MAPRE1):c.476-199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,080 control chromosomes in the GnomAD database, including 5,086 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 0.24 ( 5086 hom., cov: 32)

Consequence

MAPRE1
NM_012325.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0780
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAPRE1NM_012325.3 linkuse as main transcriptc.476-199C>T intron_variant ENST00000375571.6
MAPRE1XM_011528696.3 linkuse as main transcriptc.476-199C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAPRE1ENST00000375571.6 linkuse as main transcriptc.476-199C>T intron_variant 1 NM_012325.3 P1

Frequencies

GnomAD3 genomes
AF:
0.239
AC:
36375
AN:
151962
Hom.:
5073
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.382
Gnomad AMI
AF:
0.272
Gnomad AMR
AF:
0.217
Gnomad ASJ
AF:
0.231
Gnomad EAS
AF:
0.354
Gnomad SAS
AF:
0.300
Gnomad FIN
AF:
0.144
Gnomad MID
AF:
0.229
Gnomad NFE
AF:
0.160
Gnomad OTH
AF:
0.216
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.239
AC:
36421
AN:
152080
Hom.:
5086
Cov.:
32
AF XY:
0.242
AC XY:
17989
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.382
Gnomad4 AMR
AF:
0.217
Gnomad4 ASJ
AF:
0.231
Gnomad4 EAS
AF:
0.354
Gnomad4 SAS
AF:
0.299
Gnomad4 FIN
AF:
0.144
Gnomad4 NFE
AF:
0.160
Gnomad4 OTH
AF:
0.215
Alfa
AF:
0.204
Hom.:
619
Bravo
AF:
0.252
Asia WGS
AF:
0.260
AC:
907
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
7.5
Dann
Benign
0.78

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: rs2235760; hg19: chr20-31427342; COSMIC: COSV65032934; COSMIC: COSV65032934; API