rs1271784

Positions:

• chr18-35138633-T-A
• chr18-35138633-T-C
• chr18-35138633-T-G

Variant summary

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

The NM_014268.4(MAPRE2):​c.910-1662T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,082 control chromosomes in the GnomAD database, including 16,058 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 0.41 (16058 hom., cov: 32)
• Consequence: MAPRE2 NM_014268.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAPRE2	NM_014268.4	c.910-1662T>A		intron_variant		ENST00000300249.10	NP_055083.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPRE2	ENST00000300249.10	c.910-1662T>A		intron_variant		1	NM_014268.4	ENSP00000300249	A1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61491 AN: 151964 Hom.: 16015 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.405 AC: 61600 AN: 152082 Hom.: 16058 Cov.: 32 AF XY: 0.405 AC XY: 30114 AN XY: 74340

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.378

Alfa AF: 0.335 Hom.: 1411

Bravo AF: 0.432

Asia WGS AF: 0.465 AC: 1619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
DANN	Benign	0.72

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: rs1271784; hg19: chr18-32718597;