rs5744456
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000591.4(CD14):c.*92T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,186,312 control chromosomes in the GnomAD database, including 35 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 0.010 ( 19 hom., cov: 32)
Exomes 𝑓: 0.0010 ( 16 hom. )
Consequence
CD14
NM_000591.4 3_prime_UTR
NM_000591.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.123
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0102 (1552/152326) while in subpopulation AFR AF= 0.035 (1457/41574). AF 95% confidence interval is 0.0335. There are 19 homozygotes in gnomad4. There are 730 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 19 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD14 | NM_000591.4 | c.*92T>A | 3_prime_UTR_variant | 2/2 | ENST00000302014.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD14 | ENST00000302014.11 | c.*92T>A | 3_prime_UTR_variant | 2/2 | 1 | NM_000591.4 | P1 | ||
CD14 | ENST00000498971.7 | c.*92T>A | 3_prime_UTR_variant | 3/3 | 2 | P1 | |||
CD14 | ENST00000512545.2 | c.*92T>A | 3_prime_UTR_variant | 3/3 | 3 | P1 | |||
CD14 | ENST00000519715.2 | c.*92T>A | 3_prime_UTR_variant | 3/3 | 4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0102 AC: 1552AN: 152208Hom.: 19 Cov.: 32
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GnomAD4 exome AF: 0.00103 AC: 1068AN: 1033986Hom.: 16 Cov.: 13 AF XY: 0.000896 AC XY: 463AN XY: 516550
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GnomAD4 genome ? AF: 0.0102 AC: 1552AN: 152326Hom.: 19 Cov.: 32 AF XY: 0.00980 AC XY: 730AN XY: 74484
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at