dbSNP rs11848279: NFATC4:c.*1370A>G (chr14-24379075-A-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_004554.5(NFATC4):c.*1370A>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 0.239 in 152,178 control chromosomes in the GnomAD database, including 4,645 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 0.24 ( 4645 hom., cov: 32)

Exomes 𝑓: 0.21 ( 0 hom. )

Consequence

NFATC4
NM_004554.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0300

Publications

17 publications found

Variant links:

Genes affected

NFATC4 (HGNC:7778): (nuclear factor of activated T cells 4) This gene encodes a member of the nuclear factor of activated T cells (NFAT) protein family. The encoded protein is part of a DNA-binding transcription complex. This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor stimulation and an inducible nuclear component. NFAT proteins are activated by the calmodulin-dependent phosphatase, calcineurin. The encoded protein plays a role in the inducible expression of cytokine genes in T cells, especially in the induction of interleukin-2 and interleukin-4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

NFATC4 links:

Genome browser will be placed here

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=-0.71).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFATC4	NM_004554.5 link	c.*1370A>G		3_prime_UTR_variant	Exon 10 of 10	ENST00000250373.9	NP_004545.2	Q14934-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFATC4	ENST00000250373.9 link	c.*1370A>G		3_prime_UTR_variant	Exon 10 of 10	1	NM_004554.5	ENSP00000250373.4		Q14934-1

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36308

AN:

152018

Hom.:

4645

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.420

Gnomad SAS

AF:

0.379

Gnomad FIN

AF:

0.243

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.217

GnomAD4 exome

AF:

0.214

AC:

AN:

Hom.:

Cov.:

AF XY:

0.208

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.188

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.447

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.239

AC:

36326

AN:

152136

Hom.:

4645

Cov.:

AF XY:

0.244

AC XY:

18120

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.212

AC:

8804

AN:

41496

American (AMR)

AF:

0.308

AC:

4709

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

497

AN:

3468

East Asian (EAS)

AF:

0.420

AC:

2174

AN:

5174

South Asian (SAS)

AF:

0.378

AC:

1821

AN:

4818

European-Finnish (FIN)

AF:

0.243

AC:

2574

AN:

10596

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.223

AC:

15126

AN:

67974

Other (OTH)

AF:

0.213

AC:

450

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1409

2819

4228

5638

7047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.227

Hom.:

15760

Bravo

AF:

0.242

Asia WGS

AF:

0.392

AC:

1364

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

8.0

(source)

DANN

Benign

0.83

PhyloP100

-0.030

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs11848279

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