rs920799

Positions:

• chr18-35032574-C-A

Variant summary

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

The NM_001143827.3(MAPRE2):​c.86+27021C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,964 control chromosomes in the GnomAD database, including 16,027 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 0.46 (16027 hom., cov: 31)
• Consequence: MAPRE2 NM_001143827.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977

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 = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAPRE2	NM_001143826.3	c.-8+27021C>A		intron_variant
MAPRE2	NM_001143827.3	c.86+27021C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPRE2	ENST00000413393.5	c.-8+27021C>A		intron_variant		5		P4
MAPRE2	ENST00000436190.6	c.86+27021C>A		intron_variant		2
MAPRE2	ENST00000587359.5	c.-8+27021C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69553 AN: 151842 Hom.: 16017 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.458 AC: 69601 AN: 151964 Hom.: 16027 Cov.: 31 AF XY: 0.455 AC XY: 33790 AN XY: 74272

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.434

Alfa AF: 0.463 Hom.: 2351

Bravo AF: 0.462

Asia WGS AF: 0.354 AC: 1230 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	0.40
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs920799; hg19: chr18-32612538;