dbSNP rs7359387: NFAT5:c.*3411T>G (chr16-69699762-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

13 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:

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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=-0.83).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138713.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NFAT5	NM_138713.4	MANE Select	c.*3411T>G	3_prime_UTR	Exon 15 of 15	NP_619727.2
NFAT5	NM_001113178.3		c.*3411T>G	3_prime_UTR	Exon 15 of 15	NP_001106649.1
NFAT5	NM_006599.4		c.*3411T>G	3_prime_UTR	Exon 14 of 14	NP_006590.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NFAT5	ENST00000349945.7	TSL:1 MANE Select	c.*3411T>G	3_prime_UTR	Exon 15 of 15	ENSP00000338806.3
NFAT5	ENST00000354436.6	TSL:1	c.*3411T>G	3_prime_UTR	Exon 14 of 14	ENSP00000346420.2
NFAT5	ENST00000393742.7	TSL:1	n.*7823T>G	non_coding_transcript_exon	Exon 15 of 15	ENSP00000377343.3

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

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.143

AC:

AN:

342

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.155

AC:

23605

AN:

152160

Hom.:

1986

Cov.:

AF XY:

0.157

AC XY:

11641

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.144

AC:

5971

AN:

41526

American (AMR)

AF:

0.0955

AC:

1460

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

679

AN:

3468

East Asian (EAS)

AF:

0.364

AC:

1882

AN:

5166

South Asian (SAS)

AF:

0.192

AC:

924

AN:

4818

European-Finnish (FIN)

AF:

0.158

AC:

1670

AN:

10586

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.155

AC:

10545

AN:

67998

Other (OTH)

AF:

0.148

AC:

313

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1013

2025

3038

4050

5063

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.154

Hom.:

2171

Bravo

AF:

0.149

Asia WGS

AF:

0.237

AC:

822

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.0

(source)

DANN

Benign

0.69

PhyloP100

1.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over