rs595086

Positions:

• chr18-35044703-A-G
• chr18-35044703-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000300249.10(MAPRE2):​c.122+3042A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,158 control chromosomes in the GnomAD database, including 43,218 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 0.75 (43218 hom., cov: 32)
• Consequence: MAPRE2 ENST00000300249.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

Genes affected

MAPRE2 (HGNC:6891): (microtubule associated protein RP/EB family member 2) The protein encoded by this gene shares significant homology to the adenomatous polyposis coli (APC) protein-binding EB1 gene family. This protein is a microtubule-associated protein that is necessary for spindle symmetry during mitosis. It is thought to play a role in the tumorigenesis of colorectal cancers and the proliferative control of normal cells. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAPRE2	NM_014268.4	c.122+3042A>G		intron_variant		ENST00000300249.10	NP_055083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPRE2	ENST00000300249.10	c.122+3042A>G		intron_variant		1	NM_014268.4	ENSP00000300249	A1

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113493 AN: 152040 Hom.: 43159 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.731

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.747 AC: 113608 AN: 152158 Hom.: 43218 Cov.: 32 AF XY: 0.745 AC XY: 55427 AN XY: 74386

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.730

Alfa AF: 0.686 Hom.: 19788

Bravo AF: 0.761

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.82
DANN	Benign	0.48

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

Other links and lift over

dbSNP: rs595086; hg19: chr18-32624667;