chr16-69699557-G-A

Variant names:

• chr16-69699557-G-A
• rs7359336
• ENST00000393742.7:n.*7618G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000393742.7(NFAT5):​n.*7618G>A variant causes a non coding transcript exon 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 ENST00000393742.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.33
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NFAT5	NM_138713.4	c.*3206G>A		3_prime_UTR_variant	Exon 15 of 15	ENST00000349945.7	NP_619727.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFAT5	ENST00000349945.7	c.*3206G>A		3_prime_UTR_variant	Exon 15 of 15	1	NM_138713.4	ENSP00000338806.3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.582 AC: 248 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.750 AC: 3 AN: 4

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

African (AFR) AF: 0.783 AC: 32483 AN: 41496

American (AMR) AF: 0.650 AC: 9934 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1984 AN: 3470

East Asian (EAS) AF: 0.882 AC: 4571 AN: 5182

South Asian (SAS) AF: 0.686 AC: 3309 AN: 4822

European-Finnish (FIN) AF: 0.570 AC: 5998 AN: 10532

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39375 AN: 67964

Other (OTH) AF: 0.651 AC: 1378 AN: 2116

Alfa AF: 0.607 Hom.: 108467

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
PhyloP100		3.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7359336; hg19: chr16-69733460;