rs56368098
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_138713.4(NFAT5):āc.1969T>Gā(p.Ser657Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00231 in 1,614,096 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_138713.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFAT5 | NM_138713.4 | c.1969T>G | p.Ser657Ala | missense_variant | 13/15 | ENST00000349945.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFAT5 | ENST00000349945.7 | c.1969T>G | p.Ser657Ala | missense_variant | 13/15 | 1 | NM_138713.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00162 AC: 246AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00228 AC: 572AN: 251330Hom.: 2 AF XY: 0.00238 AC XY: 323AN XY: 135844
GnomAD4 exome AF: 0.00238 AC: 3483AN: 1461864Hom.: 12 Cov.: 32 AF XY: 0.00242 AC XY: 1763AN XY: 727230
GnomAD4 genome ? AF: 0.00162 AC: 246AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.00137 AC XY: 102AN XY: 74446
ClinVar
Submissions by phenotype
NFAT5-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 26, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Immunodeficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at