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GeneBe

8-89914707-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_001126111.3(OSGIN2):c.489C>T(p.His163=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00286 in 1,613,910 control chromosomes in the GnomAD database, including 117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 64 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 53 hom. )

Consequence

OSGIN2
NM_001126111.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.109
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 8-89914707-C-T is Benign according to our data. Variant chr8-89914707-C-T is described in ClinVar as [Benign]. Clinvar id is 784133.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.109 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0543 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OSGIN2NM_001126111.3 linkuse as main transcriptc.489C>T p.His163= synonymous_variant 4/6 ENST00000451899.7
OSGIN2NM_004337.2 linkuse as main transcriptc.357C>T p.His119= synonymous_variant 4/6
OSGIN2XM_011517287.4 linkuse as main transcriptc.357C>T p.His119= synonymous_variant 4/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OSGIN2ENST00000451899.7 linkuse as main transcriptc.489C>T p.His163= synonymous_variant 4/61 NM_001126111.3 Q9Y236-2
OSGIN2ENST00000297438.6 linkuse as main transcriptc.357C>T p.His119= synonymous_variant 4/61 P1Q9Y236-1
OSGIN2ENST00000647849.1 linkuse as main transcriptc.357C>T p.His119= synonymous_variant 4/6 P1Q9Y236-1
OSGIN2ENST00000520659.1 linkuse as main transcriptc.489C>T p.His163= synonymous_variant 4/52

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0161
AC:
2447
AN:
152190
Hom.:
63
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0562
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00615
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:
0.000132
Gnomad OTH
AF:
0.00670
GnomAD3 exomes
AF:
0.00379
AC:
952
AN:
251294
Hom.:
25
AF XY:
0.00270
AC XY:
367
AN XY:
135826
show subpopulations
Gnomad AFR exome
AF:
0.0535
Gnomad AMR exome
AF:
0.00202
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000440
Gnomad OTH exome
AF:
0.000815
GnomAD4 exome
AF:
0.00148
AC:
2157
AN:
1461602
Hom.:
53
Cov.:
31
AF XY:
0.00128
AC XY:
934
AN XY:
727110
show subpopulations
Gnomad4 AFR exome
AF:
0.0551
Gnomad4 AMR exome
AF:
0.00264
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000189
Gnomad4 OTH exome
AF:
0.00270
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0161
AC:
2455
AN:
152308
Hom.:
64
Cov.:
32
AF XY:
0.0155
AC XY:
1151
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.0562
Gnomad4 AMR
AF:
0.00614
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000132
Gnomad4 OTH
AF:
0.00664
Alfa
AF:
0.00740
Hom.:
11
Bravo
AF:
0.0178
Asia WGS
AF:
0.00115
AC:
4
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000119

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 submitterclinical testingInvitaeJul 16, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.28
Cadd
Benign
11
Dann
Benign
0.63
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs77303215; hg19: chr8-90926935; API