20-32855130-A-G

Variant names:

• chr20-32855130-A-G
• rs17297652
• ENST00000908452.1:c.*48-988A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000908452.1(MAPRE1):​c.*48-988A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.026 in 152,282 control chromosomes in the GnomAD database, including 71 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 0.026 (71 hom., cov: 32)
• Consequence: MAPRE1 ENST00000908452.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.026 (3956/152282) while in subpopulation NFE AF = 0.0399 (2711/68024). AF 95% confidence interval is 0.0386. There are 71 homozygotes in GnomAd4. There are 1901 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High AC in GnomAd4 at 3956 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000908452.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPRE1	ENST00000908452.1		c.*48-988A>G		intron	N/A	ENSP00000578511.1

Frequencies

GnomAD3 genomes AF: 0.0260 AC: 3960 AN: 152164 Hom.: 71 Cov.: 32

Gnomad AFR AF: 0.00654

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00352

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0260 AC: 3956 AN: 152282 Hom.: 71 Cov.: 32 AF XY: 0.0255 AC XY: 1901 AN XY: 74460

African (AFR) AF: 0.00652 AC: 271 AN: 41570

American (AMR) AF: 0.0204 AC: 311 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.00353 AC: 17 AN: 4820

European-Finnish (FIN) AF: 0.0446 AC: 473 AN: 10610

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0399 AC: 2711 AN: 68024

Other (OTH) AF: 0.0223 AC: 47 AN: 2110

Alfa AF: 0.0341 Hom.: 14

Bravo AF: 0.0229

Asia WGS AF: 0.00115 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.5
DANN	Benign	0.89
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs17297652; hg19: chr20-31442936;