chr8-143567282-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001100878.2(MROH6):​c.2117G>T​(p.Ser706Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000934 in 1,070,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 9.3e-7 ( 0 hom. )

Consequence

MROH6
NM_001100878.2 missense

Scores

1
4
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.20
Variant links:
Genes affected
MROH6 (HGNC:27814): (maestro heat like repeat family member 6)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.18737552).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MROH6NM_001100878.2 linkc.2117G>T p.Ser706Ile missense_variant Exon 14 of 14 ENST00000398882.8 NP_001094348.1 A6NGR9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MROH6ENST00000398882.8 linkc.2117G>T p.Ser706Ile missense_variant Exon 14 of 14 5 NM_001100878.2 ENSP00000381857.3 A6NGR9

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
9.34e-7
AC:
1
AN:
1070926
Hom.:
0
Cov.:
30
AF XY:
0.00000198
AC XY:
1
AN XY:
505618
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000123
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
May 14, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.2117G>T (p.S706I) alteration is located in exon 14 (coding exon 14) of the MROH6 gene. This alteration results from a G to T substitution at nucleotide position 2117, causing the serine (S) at amino acid position 706 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
-0.046
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
22
DANN
Uncertain
0.97
DEOGEN2
Benign
0.017
T;.;.;.
Eigen
Benign
0.017
Eigen_PC
Benign
-0.092
FATHMM_MKL
Benign
0.080
N
LIST_S2
Benign
0.46
.;.;.;T
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.19
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.8
L;.;.;.
PrimateAI
Uncertain
0.76
T
PROVEAN
Uncertain
-2.6
D;D;D;D
REVEL
Benign
0.13
Sift
Uncertain
0.0030
D;T;T;T
Sift4G
Pathogenic
0.0
D;D;D;D
Polyphen
1.0
D;.;.;.
Vest4
0.25
MutPred
0.17
Loss of phosphorylation at S706 (P = 0.0242);.;.;.;
MVP
0.15
MPC
0.062
ClinPred
0.84
D
GERP RS
5.0
Varity_R
0.30
gMVP
0.34

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-144649452; API