rs1054283
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_016010.3(ZC2HC1A):āc.666A>Gā(p.Leu222=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,610,586 control chromosomes in the GnomAD database, including 443,631 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: š 0.69 ( 36586 hom., cov: 32)
Exomes š: 0.74 ( 407045 hom. )
Consequence
ZC2HC1A
NM_016010.3 synonymous
NM_016010.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.377
Genes affected
ZC2HC1A (HGNC:24277): (zinc finger C2HC-type containing 1A) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]
IL7 (HGNC:6023): (interleukin 7) The protein encoded by this gene is a cytokine important for B and T cell development. This cytokine and the hepatocyte growth factor (HGF) form a heterodimer that functions as a pre-pro-B cell growth-stimulating factor. IL7 is found to be a cofactor for V(D)J rearrangement of the T cell receptor beta (TCRB) during early T cell development. This cytokine can be produced locally by intestinal epithelial and epithelial goblet cells, and may serve as a regulatory factor for intestinal mucosal lymphocytes. IL7 plays an essential role in lymphoid cell survival, and in the maintenance of naive and memory T cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional splice variants have been described but their presence in normal tissues has not been confirmed. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can be a potent inducer of proinflammatory cytokines and chemokines which may defend against the infection, but may also mediate destructive lung injury. Elevated serum IL7 levels, together with several other circulating cytokines and chemokines, has been found to be associated with the severity of Coronavirus Disease 19 (COVID-19). [provided by RefSeq, Jul 2020]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP7
?
Synonymous conserved (PhyloP=0.377 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC2HC1A | NM_016010.3 | c.666A>G | p.Leu222= | synonymous_variant | 7/9 | ENST00000263849.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC2HC1A | ENST00000263849.9 | c.666A>G | p.Leu222= | synonymous_variant | 7/9 | 1 | NM_016010.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.686 AC: 104184AN: 151916Hom.: 36568 Cov.: 32
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GnomAD3 exomes AF: 0.743 AC: 185922AN: 250396Hom.: 70173 AF XY: 0.742 AC XY: 100493AN XY: 135390
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GnomAD4 exome AF: 0.745 AC: 1086231AN: 1458552Hom.: 407045 Cov.: 40 AF XY: 0.745 AC XY: 540429AN XY: 725712
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GnomAD4 genome ? AF: 0.686 AC: 104246AN: 152034Hom.: 36586 Cov.: 32 AF XY: 0.688 AC XY: 51104AN XY: 74292
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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