Variant 16-68122699-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_173165.3(NFATC3):c.816G>A(p.Gly272=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00649 in 1,614,192 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0054 ( 3 hom., cov: 31)

Exomes 𝑓: 0.0066 ( 36 hom. )

Consequence

NFATC3
NM_173165.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.72

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 -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 16-68122699-G-A is Benign according to our data. Variant chr16-68122699-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 782312.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.72 with no splicing effect.

BS2

High AC in GnomAd4 at 817 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
NFATC3	NM_173165.3 linkuse as main transcript	c.816G>A	p.Gly272=	synonymous_variant	2/10	ENST00000346183.8
NFATC3	NM_004555.4 linkuse as main transcript	c.816G>A	p.Gly272=	synonymous_variant	2/11
NFATC3	NM_173163.3 linkuse as main transcript	c.816G>A	p.Gly272=	synonymous_variant	2/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFATC3	ENST00000346183.8 linkuse as main transcript	c.816G>A	p.Gly272=	synonymous_variant	2/10	1	NM_173165.3	P3	Q12968-1

Frequencies

GnomAD3 genomes

AF:

0.00538

AC:

819

AN:

152204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00174

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00733

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00395

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00841

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00497

AC:

1250

AN:

251264

Hom.:

AF XY:

0.00491

AC XY:

667

AN XY:

135792

show subpopulations

Gnomad AFR exome

AF:

0.00178

Gnomad AMR exome

AF:

0.00659

Gnomad ASJ exome

AF:

0.00159

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000980

Gnomad FIN exome

AF:

0.00338

Gnomad NFE exome

AF:

0.00752

Gnomad OTH exome

AF:

0.00767

GnomAD4 exome

AF:

0.00661

AC:

9667

AN:

1461870

Hom.:

Cov.:

AF XY:

0.00663

AC XY:

4823

AN XY:

727238

show subpopulations

Gnomad4 AFR exome

AF:

0.00143

Gnomad4 AMR exome

AF:

0.00718

Gnomad4 ASJ exome

AF:

0.00214

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000927

Gnomad4 FIN exome

AF:

0.00298

Gnomad4 NFE exome

AF:

0.00782

Gnomad4 OTH exome

AF:

0.00594

GnomAD4 genome

AF:

0.00536

AC:

817

AN:

152322

Hom.:

Cov.:

AF XY:

0.00517

AC XY:

385

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00173

Gnomad4 AMR

AF:

0.00732

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00395

Gnomad4 NFE

AF:

0.00838

Gnomad4 OTH

AF:

0.00425

Alfa

AF:

0.00662

Hom.:

Bravo

AF:

0.00571

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00883

EpiControl

AF:

0.00871

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2022	NFATC3: BP4, BP7, BS2 -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jul 27, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

6.7

DANN

Benign

0.79

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over