Variant rs12598 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000346183.8(NFATC3):c.2943G>A(p.Thr981=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 1,614,022 control chromosomes in the GnomAD database, including 6,166 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 0.057 ( 330 hom., cov: 31)

Exomes 𝑓: 0.084 ( 5836 hom. )

Consequence

NFATC3
ENST00000346183.8 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.385

Variant links:

Genes affected

NFATC3 (HGNC:7777): (nuclear factor of activated T cells 3) The product of this gene is a member of the nuclear factors of activated T cells 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 (TCR) stimulation and an inducible nuclear component. Other members of this family participate to form this complex also. The product of this gene plays a role in the regulation of gene expression in T cells and immature thymocytes. Several transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Nov 2010]

NFATC3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP7

Synonymous conserved (PhyloP=-0.385 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
NFATC3	NM_173165.3 linkuse as main transcript	c.2943G>A	p.Thr981=	synonymous_variant	9/10	ENST00000346183.8	NP_775188.1
NFATC3	NM_004555.4 linkuse as main transcript	c.2943G>A	p.Thr981=	synonymous_variant	9/11		NP_004546.1
NFATC3	NM_173163.3 linkuse as main transcript	c.2943G>A	p.Thr981=	synonymous_variant	9/11		NP_775186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NFATC3	ENST00000346183.8 linkuse as main transcript	c.2943G>A	p.Thr981=	synonymous_variant	9/10	1	NM_173165.3	ENSP00000300659	P3	Q12968-1

Frequencies

GnomAD3 genomes

AF:

0.0569

AC:

8643

AN:

152026

Hom.:

330

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0156

Gnomad AMI

AF:

0.0242

Gnomad AMR

AF:

0.0268

Gnomad ASJ

AF:

0.0260

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0699

Gnomad FIN

AF:

0.0821

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0910

Gnomad OTH

AF:

0.0344

GnomAD3 exomes

AF:

0.0633

AC:

15909

AN:

251466

Hom.:

722

AF XY:

0.0662

AC XY:

8998

AN XY:

135906

show subpopulations

Gnomad AFR exome

AF:

0.0139

Gnomad AMR exome

AF:

0.0204

Gnomad ASJ exome

AF:

0.0256

Gnomad EAS exome

AF:

0.000652

Gnomad SAS exome

AF:

0.0778

Gnomad FIN exome

AF:

0.0818

Gnomad NFE exome

AF:

0.0896

Gnomad OTH exome

AF:

0.0600

GnomAD4 exome

AF:

0.0844

AC:

123428

AN:

1461878

Hom.:

5836

Cov.:

AF XY:

0.0839

AC XY:

61041

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.0122

Gnomad4 AMR exome

AF:

0.0206

Gnomad4 ASJ exome

AF:

0.0254

Gnomad4 EAS exome

AF:

0.000705

Gnomad4 SAS exome

AF:

0.0784

Gnomad4 FIN exome

AF:

0.0804

Gnomad4 NFE exome

AF:

0.0954

Gnomad4 OTH exome

AF:

0.0674

GnomAD4 genome

AF:

0.0568

AC:

8642

AN:

152144

Hom.:

330

Cov.:

AF XY:

0.0551

AC XY:

4096

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.0155

Gnomad4 AMR

AF:

0.0267

Gnomad4 ASJ

AF:

0.0260

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0705

Gnomad4 FIN

AF:

0.0821

Gnomad4 NFE

AF:

0.0910

Gnomad4 OTH

AF:

0.0341

Alfa

AF:

0.0794

Hom.:

971

Bravo

AF:

0.0506

Asia WGS

AF:

0.0250

AC:

AN:

3478

EpiCase

AF:

0.0829

EpiControl

AF:

0.0803

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

8.0

DANN

Benign

0.72

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over