rs7359336

Positions:

• chr16-69699557-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138713.4(NFAT5):​c.*3206G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,502 control chromosomes in the GnomAD database, including 33,559 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 0.66 (33483 hom., cov: 32)
  • Exomes 𝑓: 0.59 (76 hom.)
• Consequence: NFAT5 NM_138713.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.33

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFAT5	NM_138713.4	c.*3206G>A		3_prime_UTR_variant	15/15	ENST00000349945.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFAT5	ENST00000349945.7	c.*3206G>A		3_prime_UTR_variant	15/15	1	NM_138713.4	A2

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99668 AN: 151952 Hom.: 33429 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.649

GnomAD4 exome AF: 0.586 AC: 253 AN: 432 Hom.: 76 Cov.: 0 AF XY: 0.588 AC XY: 153 AN XY: 260

Gnomad4 FIN exome AF: 0.582

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.656 AC: 99792 AN: 152070 Hom.: 33483 Cov.: 32 AF XY: 0.657 AC XY: 48825 AN XY: 74306

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.651

Alfa AF: 0.600 Hom.: 45104

Bravo AF: 0.670

Asia WGS AF: 0.729 AC: 2530 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7359336; hg19: chr16-69733460;