rs7270085

chr20-32849801-G-A

Variant summary

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

The NM_012325.3(MAPRE1):c.*1073G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 152,616 control chromosomes in the GnomAD database, including 533 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 0.058 (533 hom., cov: 32)
  • Exomes 𝑓: 0.013 (0 hom.)
• Consequence: MAPRE1 NM_012325.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAPRE1	NM_012325.3	c.*1073G>A		3_prime_UTR_variant	7/7	ENST00000375571.6
MAPRE1	XM_011528696.3	c.*1073G>A		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPRE1	ENST00000375571.6	c.*1073G>A		3_prime_UTR_variant	7/7	1	NM_012325.3	P1
	ENST00000565572.1	n.80+4377C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0580 AC: 8813 AN: 152046 Hom.: 532 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0235

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0448

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0193

Gnomad OTH AF: 0.0331

GnomAD4 exome AF: 0.0133 AC: 6 AN: 452 Hom.: 0 Cov.: 0 AF XY: 0.0184 AC XY: 5 AN XY: 272

Gnomad4 FIN exome AF: 0.0140

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0580 AC: 8827 AN: 152164 Hom.: 533 Cov.: 32 AF XY: 0.0574 AC XY: 4271 AN XY: 74406

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.0233

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0440

Gnomad4 FIN AF: 0.0167

Gnomad4 NFE AF: 0.0193

Gnomad4 OTH AF: 0.0328

Alfa AF: 0.0324 Hom.: 49

Bravo AF: 0.0616

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	6.5
Dann	Benign	0.85
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0

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: rs7270085; hg19: chr20-31437607;