rs9282638
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005191.4(CD80):c.101-56A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,411,842 control chromosomes in the GnomAD database, including 15,266 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 ( 2206 hom., cov: 32)
Exomes 𝑓: 0.14 ( 13060 hom. )
Consequence
CD80
NM_005191.4 intron
NM_005191.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.45
Genes affected
CD80 (HGNC:1700): (CD80 molecule) The protein encoded by this gene is a membrane receptor that is activated by the binding of CD28 or CTLA-4. The activated protein induces T-cell proliferation and cytokine production. This protein can act as a receptor for adenovirus subgroup B and may play a role in lupus neuropathy. [provided by RefSeq, Aug 2011]
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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=-1.01).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD80 | NM_005191.4 | c.101-56A>G | intron_variant | ENST00000264246.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD80 | ENST00000264246.8 | c.101-56A>G | intron_variant | 1 | NM_005191.4 | P2 | |||
CD80 | ENST00000383669.3 | c.101-56A>G | intron_variant | 1 | A2 | ||||
CD80 | ENST00000478182.5 | c.101-56A>G | intron_variant | 1 | P2 | ||||
CD80 | ENST00000463729.1 | n.213-56A>G | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.160 AC: 24377AN: 152056Hom.: 2204 Cov.: 32
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GnomAD4 exome AF: 0.138 AC: 173342AN: 1259668Hom.: 13060 AF XY: 0.135 AC XY: 84113AN XY: 625004
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GnomAD4 genome ? AF: 0.160 AC: 24393AN: 152174Hom.: 2206 Cov.: 32 AF XY: 0.160 AC XY: 11922AN XY: 74410
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ClinVar
Not reported inComputational scores
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Name
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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