1-186383149-C-G

Variant summary

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

The NM_017847.6(ODR4):ā€‹c.227C>Gā€‹(p.Ala76Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000033 in 1,543,764 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000026 ( 0 hom., cov: 32)
Exomes š‘“: 0.000034 ( 0 hom. )

Consequence

ODR4
NM_017847.6 missense

Scores

4
7
7

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.80
Variant links:
Genes affected
ODR4 (HGNC:24299): (odr-4 GPCR localization factor homolog) Predicted to be involved in protein localization. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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/exons MANE Protein UniProt
ODR4NM_017847.6 linkuse as main transcriptc.227C>G p.Ala76Gly missense_variant 3/14 ENST00000287859.11 NP_060317.3 Q5SWX8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ODR4ENST00000287859.11 linkuse as main transcriptc.227C>G p.Ala76Gly missense_variant 3/141 NM_017847.6 ENSP00000287859.6 Q5SWX8-1
ODR4ENST00000367470.8 linkuse as main transcriptc.227C>G p.Ala76Gly missense_variant 3/135 ENSP00000356440.3 Q5SWX8-2
ODR4ENST00000419367.8 linkuse as main transcriptc.227C>G p.Ala76Gly missense_variant 3/132 ENSP00000395084.3 Q5SWX8-4

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152098
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000120
AC:
18
AN:
149854
Hom.:
0
AF XY:
0.000127
AC XY:
10
AN XY:
78624
show subpopulations
Gnomad AFR exome
AF:
0.000121
Gnomad AMR exome
AF:
0.000592
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000501
Gnomad OTH exome
AF:
0.000235
GnomAD4 exome
AF:
0.0000338
AC:
47
AN:
1391666
Hom.:
0
Cov.:
31
AF XY:
0.0000423
AC XY:
29
AN XY:
686234
show subpopulations
Gnomad4 AFR exome
AF:
0.0000323
Gnomad4 AMR exome
AF:
0.000516
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:
0.0000176
Gnomad4 OTH exome
AF:
0.000173
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152098
Hom.:
0
Cov.:
32
AF XY:
0.0000269
AC XY:
2
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000655
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.000478
Alfa
AF:
0.0000434
Hom.:
0
Bravo
AF:
0.0000718
ExAC
AF:
0.0000554
AC:
5

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsSep 30, 2021The c.227C>G (p.A76G) alteration is located in exon 3 (coding exon 2) of the C1orf27 gene. This alteration results from a C to G substitution at nucleotide position 227, causing the alanine (A) at amino acid position 76 to be replaced by a glycine (G). 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
0.18
BayesDel_addAF
Benign
-0.099
T
BayesDel_noAF
Uncertain
-0.020
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.11
.;.;T
Eigen
Pathogenic
0.71
Eigen_PC
Uncertain
0.65
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Benign
0.77
T;T;T
M_CAP
Benign
0.041
D
MetaRNN
Uncertain
0.72
D;D;D
MetaSVM
Benign
-0.37
T
MutationAssessor
Uncertain
2.8
M;M;M
PROVEAN
Uncertain
-3.8
D;D;D
REVEL
Uncertain
0.38
Sift
Pathogenic
0.0
D;D;D
Sift4G
Pathogenic
0.0
D;D;D
Polyphen
1.0
.;D;D
Vest4
0.73
MVP
0.54
MPC
0.59
ClinPred
0.78
D
GERP RS
4.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.79
gMVP
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs776469582; hg19: chr1-186352281; API