rs187531871

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001394639.1(MROH2A):​c.879C>G​(p.Asn293Lys) variant causes a missense 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. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. N293N) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Consequence

MROH2A
NM_001394639.1 missense

Scores

17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.716
Variant links:
Genes affected
MROH2A (HGNC:27936): (maestro heat like repeat family member 2A) This gene encodes a HEAT-domain-containing protein. The function of the encoded protein has not been characterized. [provided by RefSeq, Aug 2016]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MROH2ANM_001394639.1 linkc.879C>G p.Asn293Lys missense_variant Exon 8 of 42 ENST00000389758.4 NP_001381568.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MROH2AENST00000389758.4 linkc.879C>G p.Asn293Lys missense_variant Exon 8 of 42 5 NM_001394639.1 ENSP00000374408.3 A6NES4
MROH2AENST00000610772.4 linkc.879C>G p.Asn293Lys missense_variant Exon 8 of 42 5 ENSP00000477597.1 A0A087WT58

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.54
CADD
Benign
5.2
DANN
Benign
0.95
DEOGEN2
Benign
0.00033
.;T
Eigen
Benign
-0.90
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.016
N
LIST_S2
Benign
0.65
T;T
M_CAP
Benign
0.044
D
MetaRNN
Benign
0.094
T;T
MetaSVM
Benign
-0.86
T
PROVEAN
Benign
-1.9
.;N
REVEL
Benign
0.11
Sift
Benign
0.23
.;T
Sift4G
Benign
0.13
T;T
Vest4
0.23
MutPred
0.57
Gain of ubiquitination at N293 (P = 0.0146);Gain of ubiquitination at N293 (P = 0.0146);
MVP
0.081
MPC
.;2.46197207718E-4
ClinPred
0.12
T
GERP RS
-2.7
Varity_R
0.032
gMVP
0.095

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.71
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.71
Position offset: 1

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-234703065; API