chr8-89924933-G-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001126111.3(OSGIN2):c.1051G>T(p.Val351Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
OSGIN2
NM_001126111.3 missense
NM_001126111.3 missense
Scores
3
10
6
Clinical Significance
Conservation
PhyloP100: 5.91
Genes affected
OSGIN2 (HGNC:1355): (oxidative stress induced growth inhibitor family member 2) Predicted to enable growth factor activity. Predicted to be involved in negative regulation of cell growth. [provided by Alliance of Genome Resources, Apr 2022]
NBN (HGNC:7652): (nibrin) Mutations in this gene are associated with Nijmegen breakage syndrome, an autosomal recessive chromosomal instability syndrome characterized by microcephaly, growth retardation, immunodeficiency, and cancer predisposition. The encoded protein is a member of the MRE11/RAD50 double-strand break repair complex which consists of 5 proteins. This gene product is thought to be involved in DNA double-strand break repair and DNA damage-induced checkpoint activation. [provided by RefSeq, Jul 2008]
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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 |
---|---|---|---|---|---|---|---|---|
OSGIN2 | NM_001126111.3 | c.1051G>T | p.Val351Leu | missense_variant | 6/6 | ENST00000451899.7 | NP_001119583.1 | |
OSGIN2 | NM_004337.2 | c.919G>T | p.Val307Leu | missense_variant | 6/6 | NP_004328.1 | ||
OSGIN2 | XM_011517287.4 | c.919G>T | p.Val307Leu | missense_variant | 6/6 | XP_011515589.1 | ||
OSGIN2 | XM_011517288.4 | c.520G>T | p.Val174Leu | missense_variant | 3/3 | XP_011515590.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OSGIN2 | ENST00000451899.7 | c.1051G>T | p.Val351Leu | missense_variant | 6/6 | 1 | NM_001126111.3 | ENSP00000396445 | ||
OSGIN2 | ENST00000297438.6 | c.919G>T | p.Val307Leu | missense_variant | 6/6 | 1 | ENSP00000297438 | P1 | ||
OSGIN2 | ENST00000647849.1 | c.919G>T | p.Val307Leu | missense_variant | 6/6 | ENSP00000497119 | P1 | |||
NBN | ENST00000697292.1 | c.*447C>A | 3_prime_UTR_variant | 17/17 | ENSP00000513229 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
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 07, 2024 | The c.1051G>T (p.V351L) alteration is located in exon 6 (coding exon 6) of the OSGIN2 gene. This alteration results from a G to T substitution at nucleotide position 1051, causing the valine (V) at amino acid position 351 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
.;T;T
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
.;N;N
REVEL
Uncertain
Sift
Uncertain
.;D;D
Sift4G
Uncertain
.;D;D
Polyphen
D;D;D
Vest4
0.53, 0.53
MutPred
Gain of sheet (P = 0.0477);Gain of sheet (P = 0.0477);.;
MVP
0.46
MPC
0.69
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.