ENST00000393742.7:n.*12004G>C – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000393742.7(NFAT5):n.*12004G>C 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 0.0922 in 152,454 control chromosomes in the GnomAD database, including 892 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 0.092 ( 889 hom., cov: 32)

Exomes 𝑓: 0.14 ( 3 hom. )

Consequence

NFAT5
ENST00000393742.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0410

Publications

9 publications found

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:

ENSG00000260772 (HGNC:):

ENSG00000260772 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFAT5	NM_138713.4 link	c.*7592G>C		3_prime_UTR_variant	Exon 15 of 15	ENST00000349945.7	NP_619727.2	O94916-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFAT5	ENST00000349945.7 link	c.*7592G>C		3_prime_UTR_variant	Exon 15 of 15	1	NM_138713.4	ENSP00000338806.3		O94916-5

Frequencies

GnomAD3 genomes

AF:

0.0921

AC:

14001

AN:

151948

Hom.:

887

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0444

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.0499

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.331

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0997

Gnomad OTH

AF:

0.0881

GnomAD4 exome

AF:

0.144

AC:

AN:

388

Hom.:

Cov.:

AF XY:

0.144

AC XY:

AN XY:

250

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.146

AC:

AN:

350

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.156

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0921

AC:

14004

AN:

152066

Hom.:

889

Cov.:

AF XY:

0.0944

AC XY:

7016

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.0445

AC:

1846

AN:

41476

American (AMR)

AF:

0.0498

AC:

760

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.158

AC:

547

AN:

3470

East Asian (EAS)

AF:

0.332

AC:

1717

AN:

5178

South Asian (SAS)

AF:

0.118

AC:

569

AN:

4828

European-Finnish (FIN)

AF:

0.139

AC:

1465

AN:

10556

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0997

AC:

6779

AN:

67978

Other (OTH)

AF:

0.0863

AC:

182

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

638

1275

1913

2550

3188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.102

Hom.:

122

Bravo

AF:

0.0841

Asia WGS

AF:

0.169

AC:

586

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.2

(source)

DANN

Benign

0.61

PhyloP100

-0.041

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over