1-186406208-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017847.6(ODR4):c.1126G>A(p.Glu376Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000601 in 1,611,400 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00058 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00060 ( 1 hom. )
Consequence
ODR4
NM_017847.6 missense
NM_017847.6 missense
Scores
4
8
6
Clinical Significance
Conservation
PhyloP100: 6.74
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]
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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=0.20984805).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ODR4 | NM_017847.6 | c.1126G>A | p.Glu376Lys | missense_variant | 12/14 | ENST00000287859.11 | NP_060317.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ODR4 | ENST00000287859.11 | c.1126G>A | p.Glu376Lys | missense_variant | 12/14 | 1 | NM_017847.6 | ENSP00000287859.6 | ||
ODR4 | ENST00000367470.8 | c.1057G>A | p.Glu353Lys | missense_variant | 11/13 | 5 | ENSP00000356440.3 | |||
ODR4 | ENST00000419367.8 | c.1030G>A | p.Glu344Lys | missense_variant | 11/13 | 2 | ENSP00000395084.3 | |||
ODR4 | ENST00000478571.1 | n.239G>A | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000578 AC: 88AN: 152152Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000587 AC: 145AN: 246878Hom.: 0 AF XY: 0.000612 AC XY: 82AN XY: 133974
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GnomAD4 exome AF: 0.000603 AC: 880AN: 1459130Hom.: 1 Cov.: 30 AF XY: 0.000599 AC XY: 435AN XY: 725844
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GnomAD4 genome AF: 0.000578 AC: 88AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74446
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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 submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.1126G>A (p.E376K) alteration is located in exon 12 (coding exon 11) of the C1orf27 gene. This alteration results from a G to A substitution at nucleotide position 1126, causing the glutamic acid (E) at amino acid position 376 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
.;.;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;.;M
PROVEAN
Uncertain
D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
1.0
.;D;D
Vest4
MVP
MPC
0.62
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at