Variant chr16-69699762-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_138713.4(NFAT5):c.*3411T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,508 control chromosomes in the GnomAD database, including 1,990 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 0.16 ( 1986 hom., cov: 32)

Exomes 𝑓: 0.14 ( 4 hom. )

Consequence

NFAT5
NM_138713.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.21

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]

NFAT5 links:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NFAT5	NM_138713.4 link	c.*3411T>G		3_prime_UTR_variant	15/15	ENST00000349945.7	NP_619727.2	O94916-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFAT5	ENST00000349945.7 link	c.*3411T>G		3_prime_UTR_variant	15/15	1	NM_138713.4	ENSP00000338806.3		O94916-5

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

23581

AN:

152042

Hom.:

1981

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.0957

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.147

GnomAD4 exome

AF:

0.141

AC:

AN:

348

Hom.:

Cov.:

AF XY:

0.139

AC XY:

AN XY:

216

show subpopulations

Gnomad4 FIN exome

AF:

0.143

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.155

AC:

23605

AN:

152160

Hom.:

1986

Cov.:

AF XY:

0.157

AC XY:

11641

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.144

Gnomad4 AMR

AF:

0.0955

Gnomad4 ASJ

AF:

0.196

Gnomad4 EAS

AF:

0.364

Gnomad4 SAS

AF:

0.192

Gnomad4 FIN

AF:

0.158

Gnomad4 NFE

AF:

0.155

Gnomad4 OTH

AF:

0.148

Alfa

AF:

0.156

Hom.:

1854

Bravo

AF:

0.149

Asia WGS

AF:

0.237

AC:

822

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.0

DANN

Benign

0.69

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over