chr8-89914707-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
NM_001126111.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.109
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP6
?
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
?
Synonymous conserved (PhyloP=0.109 with no splicing effect.
BA1
?
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 |
---|---|---|---|---|---|---|---|
OSGIN2 | NM_001126111.3 | c.489C>T | p.His163= | synonymous_variant | 4/6 | ENST00000451899.7 | |
OSGIN2 | NM_004337.2 | c.357C>T | p.His119= | synonymous_variant | 4/6 | ||
OSGIN2 | XM_011517287.4 | c.357C>T | p.His119= | synonymous_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OSGIN2 | ENST00000451899.7 | c.489C>T | p.His163= | synonymous_variant | 4/6 | 1 | NM_001126111.3 | ||
OSGIN2 | ENST00000297438.6 | c.357C>T | p.His119= | synonymous_variant | 4/6 | 1 | P1 | ||
OSGIN2 | ENST00000647849.1 | c.357C>T | p.His119= | synonymous_variant | 4/6 | P1 | |||
OSGIN2 | ENST00000520659.1 | c.489C>T | p.His163= | synonymous_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0161 AC: 2447AN: 152190Hom.: 63 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00379 AC: 952AN: 251294Hom.: 25 AF XY: 0.00270 AC XY: 367AN XY: 135826
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GnomAD4 exome AF: 0.00148 AC: 2157AN: 1461602Hom.: 53 Cov.: 31 AF XY: 0.00128 AC XY: 934AN XY: 727110
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GnomAD4 genome ? AF: 0.0161 AC: 2455AN: 152308Hom.: 64 Cov.: 32 AF XY: 0.0155 AC XY: 1151AN 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
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at