rs2569190
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001040021.3(CD14):c.-121-139T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000223 in 447,840 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
Exomes 𝑓: 0.0000022 ( 0 hom. )
Consequence
CD14
NM_001040021.3 intron
NM_001040021.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.07
Genes affected
CD14 (HGNC:1628): (CD14 molecule) The protein encoded by this gene is a surface antigen that is preferentially expressed on monocytes/macrophages. It cooperates with other proteins to mediate the innate immune response to bacterial lipopolysaccharide, and to viruses. This gene has been identified as a target candidate in the treatment of SARS-CoV-2-infected patients to potentially lessen or inhibit a severe inflammatory response. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2020]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD14 | NM_001040021.3 | c.-121-139T>G | intron_variant | NP_001035110.1 | ||||
CD14 | NM_001174104.2 | c.-221-39T>G | intron_variant | NP_001167575.1 | ||||
CD14 | NM_001174105.2 | c.-121-139T>G | intron_variant | NP_001167576.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD14 | ENST00000498971.7 | c.-121-139T>G | intron_variant | 2 | ENSP00000426543 | P1 | ||||
CD14 | ENST00000512545.2 | c.-221-39T>G | intron_variant | 3 | ENSP00000425447 | P1 | ||||
CD14 | ENST00000519715.2 | c.-121-139T>G | intron_variant | 4 | ENSP00000430884 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000223 AC: 1AN: 447840Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0AN XY: 237434
GnomAD4 exome
AF:
AC:
1
AN:
447840
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Cov.:
4
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0
AN XY:
237434
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GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
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