rs148886916
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS2
The NM_138713.4(NFAT5):āc.430A>Gā(p.Ser144Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000476 in 1,614,116 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S144N) has been classified as Uncertain significance.
Frequency
Consequence
NM_138713.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFAT5 | NM_138713.4 | c.430A>G | p.Ser144Gly | missense_variant | 4/15 | ENST00000349945.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFAT5 | ENST00000349945.7 | c.430A>G | p.Ser144Gly | missense_variant | 4/15 | 1 | NM_138713.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000466 AC: 71AN: 152214Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000493 AC: 124AN: 251284Hom.: 0 AF XY: 0.000508 AC XY: 69AN XY: 135798
GnomAD4 exome AF: 0.000477 AC: 697AN: 1461784Hom.: 0 Cov.: 31 AF XY: 0.000473 AC XY: 344AN XY: 727176
GnomAD4 genome ? AF: 0.000466 AC: 71AN: 152332Hom.: 1 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.430A>G (p.S144G) alteration is located in exon 4 (coding exon 4) of the NFAT5 gene. This alteration results from a A to G substitution at nucleotide position 430, causing the serine (S) at amino acid position 144 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Immunodeficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 07, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at