8-89924970-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001126111.3(OSGIN2):c.1088G>C(p.Cys363Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00215 in 1,613,886 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 36 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 46 hom. )
Consequence
OSGIN2
NM_001126111.3 missense
NM_001126111.3 missense
Scores
1
4
8
Clinical Significance
Conservation
PhyloP100: 4.78
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008452892).
BP6
?
Variant 8-89924970-G-C is Benign according to our data. Variant chr8-89924970-G-C is described in ClinVar as [Benign]. Clinvar id is 713505.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0119 (1810/152322) while in subpopulation AFR AF= 0.0415 (1725/41568). AF 95% confidence interval is 0.0399. There are 36 homozygotes in gnomad4. There are 877 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 36 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OSGIN2 | NM_001126111.3 | c.1088G>C | p.Cys363Ser | missense_variant | 6/6 | ENST00000451899.7 | |
OSGIN2 | NM_004337.2 | c.956G>C | p.Cys319Ser | missense_variant | 6/6 | ||
OSGIN2 | XM_011517287.4 | c.956G>C | p.Cys319Ser | missense_variant | 6/6 | ||
OSGIN2 | XM_011517288.4 | c.557G>C | p.Cys186Ser | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OSGIN2 | ENST00000451899.7 | c.1088G>C | p.Cys363Ser | missense_variant | 6/6 | 1 | NM_001126111.3 | ||
OSGIN2 | ENST00000297438.6 | c.956G>C | p.Cys319Ser | missense_variant | 6/6 | 1 | P1 | ||
OSGIN2 | ENST00000647849.1 | c.956G>C | p.Cys319Ser | missense_variant | 6/6 | P1 | |||
NBN | ENST00000697292.1 | c.*410C>G | 3_prime_UTR_variant | 17/17 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0118 AC: 1800AN: 152204Hom.: 36 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00299 AC: 749AN: 250632Hom.: 16 AF XY: 0.00206 AC XY: 279AN XY: 135418
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GnomAD4 exome AF: 0.00114 AC: 1667AN: 1461564Hom.: 46 Cov.: 32 AF XY: 0.000953 AC XY: 693AN XY: 727104
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GnomAD4 genome ? AF: 0.0119 AC: 1810AN: 152322Hom.: 36 Cov.: 32 AF XY: 0.0118 AC XY: 877AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 16, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Polyphen
D;D;D
Vest4
0.66, 0.67
MutPred
Gain of helix (P = 0.0854);Gain of helix (P = 0.0854);.;
MVP
0.19
MPC
0.67
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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