1-170983511-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001163629.2(MROH9):​c.706C>A​(p.Gln236Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00852 in 1,611,656 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0064 ( 6 hom., cov: 33)
Exomes 𝑓: 0.0087 ( 68 hom. )

Consequence

MROH9
NM_001163629.2 missense

Scores

18

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.164
Variant links:
Genes affected
MROH9 (HGNC:26287): (maestro heat like repeat family member 9)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.004406631).
BP6
Variant 1-170983511-C-A is Benign according to our data. Variant chr1-170983511-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2639546.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MROH9NM_001163629.2 linkc.706C>A p.Gln236Lys missense_variant Exon 9 of 22 ENST00000367759.9 NP_001157101.1 Q5TGP6-2
MROH9NM_025063.4 linkc.706C>A p.Gln236Lys missense_variant Exon 9 of 15 NP_079339.2 Q5TGP6-1
MROH9XM_011510005.3 linkc.706C>A p.Gln236Lys missense_variant Exon 9 of 21 XP_011508307.1
MROH9XM_011510006.3 linkc.706C>A p.Gln236Lys missense_variant Exon 9 of 21 XP_011508308.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MROH9ENST00000367759.9 linkc.706C>A p.Gln236Lys missense_variant Exon 9 of 22 5 NM_001163629.2 ENSP00000356733.4 Q5TGP6-2

Frequencies

GnomAD3 genomes
AF:
0.00640
AC:
974
AN:
152148
Hom.:
6
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00152
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00556
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.0137
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00972
Gnomad OTH
AF:
0.00718
GnomAD3 exomes
AF:
0.00626
AC:
1556
AN:
248634
Hom.:
7
AF XY:
0.00642
AC XY:
866
AN XY:
134934
show subpopulations
Gnomad AFR exome
AF:
0.00201
Gnomad AMR exome
AF:
0.00416
Gnomad ASJ exome
AF:
0.000398
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00154
Gnomad FIN exome
AF:
0.0118
Gnomad NFE exome
AF:
0.00920
Gnomad OTH exome
AF:
0.00647
GnomAD4 exome
AF:
0.00874
AC:
12755
AN:
1459390
Hom.:
68
Cov.:
29
AF XY:
0.00869
AC XY:
6312
AN XY:
726122
show subpopulations
Gnomad4 AFR exome
AF:
0.00162
Gnomad4 AMR exome
AF:
0.00419
Gnomad4 ASJ exome
AF:
0.000230
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00180
Gnomad4 FIN exome
AF:
0.0110
Gnomad4 NFE exome
AF:
0.0102
Gnomad4 OTH exome
AF:
0.00662
GnomAD4 genome
AF:
0.00640
AC:
974
AN:
152266
Hom.:
6
Cov.:
33
AF XY:
0.00650
AC XY:
484
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.00152
Gnomad4 AMR
AF:
0.00556
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.0137
Gnomad4 NFE
AF:
0.00972
Gnomad4 OTH
AF:
0.00710
Alfa
AF:
0.00873
Hom.:
8
Bravo
AF:
0.00570
TwinsUK
AF:
0.0124
AC:
46
ALSPAC
AF:
0.0106
AC:
41
ESP6500AA
AF:
0.00221
AC:
8
ESP6500EA
AF:
0.00871
AC:
71
ExAC
AF:
0.00619
AC:
748
Asia WGS
AF:
0.00116
AC:
4
AN:
3474
EpiCase
AF:
0.00830
EpiControl
AF:
0.00867

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Dec 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

MROH9: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.066
BayesDel_addAF
Benign
-0.69
T
BayesDel_noAF
Benign
-0.75
CADD
Benign
0.52
DANN
Benign
0.30
DEOGEN2
Benign
0.0059
.;T
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.011
N
LIST_S2
Benign
0.38
T;T
MetaRNN
Benign
0.0044
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.77
N;N
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-0.95
N;N
REVEL
Benign
0.015
Sift
Benign
0.92
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0080
.;B
Vest4
0.061
MVP
0.11
MPC
0.068
ClinPred
0.0013
T
GERP RS
-5.2
Varity_R
0.056
gMVP
0.097

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.16
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs112394419; hg19: chr1-170952652; API