rs39999

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_138713.4(NFAT5):​c.128-6610C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 152,190 control chromosomes in the GnomAD database, including 60,617 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 0.89 ( 60617 hom., cov: 31)

Consequence

NFAT5
NM_138713.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0950
Variant links:
Genes affected
NFAT5 (HGNC:7774): (nuclear factor of activated T cells 5) The product of this gene is a member of the nuclear factors of activated T cells family of transcription factors. Proteins belonging to this family play a central role in inducible gene transcription during the immune response. This protein regulates gene expression induced by osmotic stress in mammalian cells. Unlike monomeric members of this protein family, this protein exists as a homodimer and forms stable dimers with DNA elements. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NFAT5NM_138713.4 linkuse as main transcriptc.128-6610C>G intron_variant ENST00000349945.7 NP_619727.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NFAT5ENST00000349945.7 linkuse as main transcriptc.128-6610C>G intron_variant 1 NM_138713.4 ENSP00000338806 A2O94916-5

Frequencies

GnomAD3 genomes
AF:
0.891
AC:
135518
AN:
152072
Hom.:
60561
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.959
Gnomad AMI
AF:
0.807
Gnomad AMR
AF:
0.873
Gnomad ASJ
AF:
0.908
Gnomad EAS
AF:
0.931
Gnomad SAS
AF:
0.870
Gnomad FIN
AF:
0.866
Gnomad MID
AF:
0.946
Gnomad NFE
AF:
0.857
Gnomad OTH
AF:
0.881
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.891
AC:
135632
AN:
152190
Hom.:
60617
Cov.:
31
AF XY:
0.893
AC XY:
66461
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.959
Gnomad4 AMR
AF:
0.873
Gnomad4 ASJ
AF:
0.908
Gnomad4 EAS
AF:
0.931
Gnomad4 SAS
AF:
0.870
Gnomad4 FIN
AF:
0.866
Gnomad4 NFE
AF:
0.857
Gnomad4 OTH
AF:
0.882
Alfa
AF:
0.875
Hom.:
7261
Bravo
AF:
0.893
Asia WGS
AF:
0.897
AC:
3122
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.77
DANN
Benign
0.41

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs39999; hg19: chr16-69653696; API