rs9932251

Positions:

• chr16-68097829-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173165.3(NFATC3):​c.103+12045G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 151,956 control chromosomes in the GnomAD database, including 2,946 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 0.18 (2946 hom., cov: 31)
• Consequence: NFATC3 NM_173165.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NFATC3	NM_173165.3	c.103+12045G>A		intron_variant		ENST00000346183.8
NFATC3	NM_004555.4	c.103+12045G>A		intron_variant
NFATC3	NM_173163.3	c.103+12045G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NFATC3	ENST00000346183.8	c.103+12045G>A		intron_variant		1	NM_173165.3	P3

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27931 AN: 151838 Hom.: 2937 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.185

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.184 AC: 27974 AN: 151956 Hom.: 2946 Cov.: 31 AF XY: 0.187 AC XY: 13893 AN XY: 74266

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.189

Alfa AF: 0.151 Hom.: 1025

Bravo AF: 0.185

Asia WGS AF: 0.207 AC: 720 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	1.2
DANN	Benign	0.35

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

Other links and lift over

dbSNP: rs9932251; hg19: chr16-68131732;