rs4811191
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000609943.5(NFATC2):c.70+19064C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 152,280 control chromosomes in the GnomAD database, including 780 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 0.082 ( 780 hom., cov: 31)
Consequence
NFATC2
ENST00000609943.5 intron
ENST00000609943.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.410
Genes affected
NFATC2 (HGNC:7776): (nuclear factor of activated T cells 2) This gene is a member of the nuclear factor of activated T cells (NFAT) family. The product of this gene is a DNA-binding protein with a REL-homology region (RHR) and an NFAT-homology region (NHR). This protein is present in the cytosol and only translocates to the nucleus upon T cell receptor (TCR) stimulation, where it becomes a member of the nuclear factors of activated T cells transcription complex. This complex plays a central role in inducing gene transcription during the immune response. Alternate transcriptional splice variants encoding different isoforms have been characterized. [provided by RefSeq, Apr 2012]
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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 (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFATC2 | NM_001136021.3 | c.70+19064C>T | intron_variant | ||||
NFATC2 | NM_001258292.2 | c.70+19064C>T | intron_variant | ||||
NFATC2 | NM_001258294.2 | c.-14+19064C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFATC2 | ENST00000414705.5 | c.70+19064C>T | intron_variant | 1 | |||||
NFATC2 | ENST00000609507.1 | c.-14+19064C>T | intron_variant | 1 | |||||
NFATC2 | ENST00000609943.5 | c.70+19064C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0825 AC: 12548AN: 152160Hom.: 782 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0824 AC: 12542AN: 152280Hom.: 780 Cov.: 31 AF XY: 0.0870 AC XY: 6477AN XY: 74454
GnomAD4 genome
?
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12542
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152280
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31
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6477
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74454
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722
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at