chr14-24369722-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_004554.5(NFATC4):c.324C>T(p.Gly108=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,584,444 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0081 ( 15 hom., cov: 33)
Exomes 𝑓: 0.0010 ( 16 hom. )
Consequence
NFATC4
NM_004554.5 synonymous
NM_004554.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.30
Genes affected
NFATC4 (HGNC:7778): (nuclear factor of activated T cells 4) This gene encodes a member of the nuclear factor of activated T cells (NFAT) protein family. The encoded protein is part of a DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor stimulation and an inducible nuclear component. NFAT proteins are activated by the calmodulin-dependent phosphatase, calcineurin. The encoded protein plays a role in the inducible expression of cytokine genes in T cells, especially in the induction of interleukin-2 and interleukin-4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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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=-0.42).
BP6
?
Variant 14-24369722-C-T is Benign according to our data. Variant chr14-24369722-C-T is described in ClinVar as [Benign]. Clinvar id is 778738.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.3 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00806 (1212/150352) while in subpopulation AFR AF= 0.0269 (1117/41460). AF 95% confidence interval is 0.0256. There are 15 homozygotes in gnomad4. There are 565 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1213 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFATC4 | NM_004554.5 | c.324C>T | p.Gly108= | synonymous_variant | 2/10 | ENST00000250373.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFATC4 | ENST00000250373.9 | c.324C>T | p.Gly108= | synonymous_variant | 2/10 | 1 | NM_004554.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00807 AC: 1213AN: 150232Hom.: 15 Cov.: 33
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GnomAD3 exomes AF: 0.00244 AC: 572AN: 234280Hom.: 8 AF XY: 0.00169 AC XY: 215AN XY: 127524
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GnomAD4 exome AF: 0.00103 AC: 1472AN: 1434092Hom.: 16 Cov.: 38 AF XY: 0.000939 AC XY: 669AN XY: 712668
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GnomAD4 genome ? AF: 0.00806 AC: 1212AN: 150352Hom.: 15 Cov.: 33 AF XY: 0.00768 AC XY: 565AN XY: 73582
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 14, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at