8-89921104-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001126111.3(OSGIN2):āc.553A>Gā(p.Ile185Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000562 in 1,602,400 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 32)
Exomes š: 0.000060 ( 0 hom. )
Consequence
OSGIN2
NM_001126111.3 missense
NM_001126111.3 missense
Scores
7
12
Clinical Significance
Conservation
PhyloP100: 4.00
Genes affected
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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=0.21398893).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OSGIN2 | NM_001126111.3 | c.553A>G | p.Ile185Val | missense_variant | 5/6 | ENST00000451899.7 | NP_001119583.1 | |
OSGIN2 | NM_004337.2 | c.421A>G | p.Ile141Val | missense_variant | 5/6 | NP_004328.1 | ||
OSGIN2 | XM_011517287.4 | c.421A>G | p.Ile141Val | missense_variant | 5/6 | XP_011515589.1 | ||
OSGIN2 | XM_011517288.4 | c.22A>G | p.Ile8Val | missense_variant | 2/3 | XP_011515590.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OSGIN2 | ENST00000451899.7 | c.553A>G | p.Ile185Val | missense_variant | 5/6 | 1 | NM_001126111.3 | ENSP00000396445.2 | ||
OSGIN2 | ENST00000297438.6 | c.421A>G | p.Ile141Val | missense_variant | 5/6 | 1 | ENSP00000297438.2 | |||
OSGIN2 | ENST00000647849.1 | c.421A>G | p.Ile141Val | missense_variant | 5/6 | ENSP00000497119.1 | ||||
OSGIN2 | ENST00000520659.1 | c.553A>G | p.Ile185Val | missense_variant | 5/5 | 2 | ENSP00000431029.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152132Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000489 AC: 12AN: 245188Hom.: 0 AF XY: 0.0000528 AC XY: 7AN XY: 132542
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GnomAD4 exome AF: 0.0000600 AC: 87AN: 1450150Hom.: 0 Cov.: 27 AF XY: 0.0000679 AC XY: 49AN XY: 721788
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74456
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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 | Nov 19, 2024 | The c.553A>G (p.I185V) alteration is located in exon 5 (coding exon 5) of the OSGIN2 gene. This alteration results from a A to G substitution at nucleotide position 553, causing the isoleucine (I) at amino acid position 185 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
.;N;N;N
REVEL
Benign
Sift
Uncertain
.;D;T;T
Sift4G
Benign
.;T;T;D
Polyphen
B;B;P;.
Vest4
0.27, 0.32, 0.33
MutPred
Loss of sheet (P = 7e-04);Loss of sheet (P = 7e-04);.;.;
MVP
0.13
MPC
0.31
ClinPred
T
GERP RS
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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