GeneBe

rs1813348

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000498451.3(MPHOSPH10):​c.-162C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 35)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MPHOSPH10
ENST00000498451.3 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0670

Publications

6 publications found
Variant links:
Genes affected
MPHOSPH10 (HGNC:7213): (M-phase phosphoprotein 10) This gene encodes a protein that is phosphorylated during mitosis. The protein localizes to the nucleolus during interphase and to the chromosomes during M phase. The protein associates with the U3 small nucleolar ribonucleoprotein 60-80S complexes and may be involved in pre-rRNA processing. [provided by RefSeq, Dec 2010]
MCEE (HGNC:16732): (methylmalonyl-CoA epimerase) The product of this gene catalyzes the interconversion of D- and L-methylmalonyl-CoA during the degradation of branched chain amino acids. odd chain-length fatty acids, and other metabolites. Mutations in this gene result in methylmalonyl-CoA epimerase deficiency, which is presented as mild to moderate methylmalonic aciduria. [provided by RefSeq, Jul 2008]
MCEE Gene-Disease associations (from GenCC):
  • methylmalonic acidemia due to methylmalonyl-CoA epimerase deficiency
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498451.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MPHOSPH10
NM_005791.3
MANE Select
c.-162C>G
upstream_gene
N/ANP_005782.1O00566

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MPHOSPH10
ENST00000498451.3
TSL:1
c.-162C>G
5_prime_UTR
Exon 1 of 5ENSP00000475545.1U3KQ48
MPHOSPH10
ENST00000468427.2
TSL:4
c.-673C>G
5_prime_UTR
Exon 1 of 11ENSP00000511582.1A0A8Q3WK70
MPHOSPH10
ENST00000695484.2
n.-162C>G
non_coding_transcript_exon
Exon 1 of 11ENSP00000511956.1A0A8Q3WKH7

Frequencies

GnomAD3 genomes
Cov.:
35
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
679506
Hom.:
0
Cov.:
9
AF XY:
0.00
AC XY:
0
AN XY:
346380
African (AFR)
AF:
0.00
AC:
0
AN:
17048
American (AMR)
AF:
0.00
AC:
0
AN:
20610
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15380
East Asian (EAS)
AF:
0.00
AC:
0
AN:
32126
South Asian (SAS)
AF:
0.00
AC:
0
AN:
50926
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
34554
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2436
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
472894
Other (OTH)
AF:
0.00
AC:
0
AN:
33532
GnomAD4 genome
Cov.:
35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
11
DANN
Benign
0.74
PhyloP100
0.067
PromoterAI
0.068
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

Other links and lift over

dbSNP: rs1813348; hg19: chr2-71357634; API