1-110892713-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000560.4(CD53):c.252+180C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 582,906 control chromosomes in the GnomAD database, including 184,131 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 0.72 ( 41708 hom., cov: 31)
Exomes 𝑓: 0.81 ( 142423 hom. )
Consequence
CD53
NM_000560.4 intron
NM_000560.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.555
Genes affected
CD53 (HGNC:1686): (CD53 molecule) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins. It contributes to the transduction of CD2-generated signals in T cells and natural killer cells and has been suggested to play a role in growth regulation. Familial deficiency of this gene has been linked to an immunodeficiency associated with recurrent infectious diseases caused by bacteria, fungi and viruses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 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=-0.88).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD53 | NM_000560.4 | c.252+180C>T | intron_variant | ENST00000271324.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD53 | ENST00000271324.6 | c.252+180C>T | intron_variant | 1 | NM_000560.4 | P1 | |||
CD53 | ENST00000648608.1 | c.252+180C>T | intron_variant | P1 | |||||
CD53 | ENST00000471220.5 | n.515C>T | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
CD53 | ENST00000476408.1 | n.365+180C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.721 AC: 109530AN: 151930Hom.: 41682 Cov.: 31
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GnomAD4 exome AF: 0.809 AC: 348501AN: 430858Hom.: 142423 Cov.: 4 AF XY: 0.808 AC XY: 182876AN XY: 226334
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GnomAD4 genome ? AF: 0.721 AC: 109596AN: 152048Hom.: 41708 Cov.: 31 AF XY: 0.720 AC XY: 53542AN XY: 74354
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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