rs714513

chr2-26983606-T-C

Variant summary

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

The NM_012326.4(MAPRE3):c.-8+12804T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,098 control chromosomes in the GnomAD database, including 22,055 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 0.52 (22055 hom., cov: 32)
• Consequence: MAPRE3 NM_012326.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

Genes affected

MAPRE3 (HGNC:6892): (microtubule associated protein RP/EB family member 3) The protein encoded by this gene is a member of the RP/EB family of genes. The protein localizes to the cytoplasmic microtubule network and binds APCL, a homolog of the adenomatous polyposis coli tumor suppressor gene. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAPRE3	NM_012326.4	c.-8+12804T>C		intron_variant		ENST00000233121.7
MAPRE3	NM_001410716.1	c.-8+12804T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPRE3	ENST00000233121.7	c.-8+12804T>C		intron_variant		1	NM_012326.4	P1
	ENST00000416226.1	n.32+26170A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78937 AN: 151980 Hom.: 22050 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.519 AC: 78955 AN: 152098 Hom.: 22055 Cov.: 32 AF XY: 0.523 AC XY: 38874 AN XY: 74354

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.548

Alfa AF: 0.538 Hom.: 3335

Bravo AF: 0.489

Asia WGS AF: 0.679 AC: 2360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.2
Dann	Benign	0.82

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: rs714513; hg19: chr2-27206474;