rs2850724

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001278669.2(NFATC1):​c.127+6362T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,298 control chromosomes in the GnomAD database, including 63,248 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 0.91 ( 63248 hom., cov: 34)

Consequence

NFATC1
NM_001278669.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.67
Variant links:
Genes affected
NFATC1 (HGNC:7775): (nuclear factor of activated T cells 1) The product of this gene is a component of the nuclear factor 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. Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response. The product of this gene is an inducible nuclear component. It functions as a major molecular target for the immunosuppressive drugs such as cyclosporin A. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. Different isoforms of this protein may regulate inducible expression of different cytokine genes. [provided by RefSeq, Jul 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NFATC1NM_001278669.2 linkuse as main transcriptc.127+6362T>C intron_variant ENST00000427363.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NFATC1ENST00000427363.7 linkuse as main transcriptc.127+6362T>C intron_variant 1 NM_001278669.2 P4O95644-1

Frequencies

GnomAD3 genomes
AF:
0.911
AC:
138578
AN:
152180
Hom.:
63188
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.912
Gnomad AMI
AF:
0.884
Gnomad AMR
AF:
0.909
Gnomad ASJ
AF:
0.774
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.964
Gnomad FIN
AF:
0.956
Gnomad MID
AF:
0.815
Gnomad NFE
AF:
0.901
Gnomad OTH
AF:
0.891
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.911
AC:
138696
AN:
152298
Hom.:
63248
Cov.:
34
AF XY:
0.913
AC XY:
67988
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.912
Gnomad4 AMR
AF:
0.909
Gnomad4 ASJ
AF:
0.774
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.964
Gnomad4 FIN
AF:
0.956
Gnomad4 NFE
AF:
0.901
Gnomad4 OTH
AF:
0.892
Alfa
AF:
0.895
Hom.:
80056
Bravo
AF:
0.906
Asia WGS
AF:
0.977
AC:
3395
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.096
DANN
Benign
0.41

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.

Other links and lift over

dbSNP: rs2850724; hg19: chr18-77162713; API