rs9989899
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007237.5(SP140):c.976+448G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,110 control chromosomes in the GnomAD database, including 2,040 homozygotes. 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: 𝑓 0.16 ( 2040 hom., cov: 32)
Consequence
SP140
NM_007237.5 intron
NM_007237.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.537
Genes affected
SP140 (HGNC:17133): (SP140 nuclear body protein) This gene encodes a member of the SP100 family of proteins, which are share common domains including an N-terminal homogeneously staining region domain followed by a SP100/autoimmune regulator/NucP41/P75/deformed epidermal autoregulatory factor domain, a plant homeobox zinc finger, and a bromodomain. The encoded protein is interferon-inducible and is expressed at high levels in the nuclei of leukocytes. Variants of this gene have been associated with multiple sclerosis, Crohn's disease, and chronic lymphocytic leukemia. Alternative splicing results in multiple variants. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SP140 | NM_007237.5 | c.976+448G>A | intron_variant | ENST00000392045.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SP140 | ENST00000392045.8 | c.976+448G>A | intron_variant | 2 | NM_007237.5 | A2 | |||
SP140 | ENST00000343805.10 | c.898+448G>A | intron_variant | 1 | A2 | ||||
SP140 | ENST00000417495.7 | c.817+448G>A | intron_variant | 1 | P2 | ||||
SP140 | ENST00000420434.7 | c.976+448G>A | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.159 AC: 24157AN: 151992Hom.: 2037 Cov.: 32
GnomAD3 genomes
?
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151992
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.159 AC: 24174AN: 152110Hom.: 2040 Cov.: 32 AF XY: 0.154 AC XY: 11457AN XY: 74358
GnomAD4 genome
?
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152110
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32
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11457
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74358
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231
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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