14-24370339-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004554.5(NFATC4):c.941C>G(p.Pro314Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,548 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P314L) has been classified as Uncertain significance.
Frequency
Consequence
NM_004554.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFATC4 | NM_004554.5 | c.941C>G | p.Pro314Arg | missense_variant | 2/10 | ENST00000250373.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFATC4 | ENST00000250373.9 | c.941C>G | p.Pro314Arg | missense_variant | 2/10 | 1 | NM_004554.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000403 AC: 10AN: 247932Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 134978
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461224Hom.: 0 Cov.: 34 AF XY: 0.0000179 AC XY: 13AN XY: 726880
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2023 | The c.941C>G (p.P314R) alteration is located in exon 2 (coding exon 2) of the NFATC4 gene. This alteration results from a C to G substitution at nucleotide position 941, causing the proline (P) at amino acid position 314 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at