16-68168844-C-T

Variant names:

• chr16-68168844-C-T
• rs4359427
• NM_173165.3:c.1774+1829C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173165.3(NFATC3):​c.1774+1829C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,064 control chromosomes in the GnomAD database, including 2,931 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 (2931 hom., cov: 32)
• Consequence: NFATC3 NM_173165.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFATC3	NM_173165.3	c.1774+1829C>T		intron_variant	Intron 5 of 9	ENST00000346183.8	NP_775188.1
NFATC3	NM_004555.4	c.1774+1829C>T		intron_variant	Intron 5 of 10		NP_004546.1
NFATC3	NM_173163.3	c.1774+1829C>T		intron_variant	Intron 5 of 10		NP_775186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFATC3	ENST00000346183.8	c.1774+1829C>T		intron_variant	Intron 5 of 9	1	NM_173165.3	ENSP00000300659.5

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27797 AN: 151946 Hom.: 2922 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.183 AC: 27840 AN: 152064 Hom.: 2931 Cov.: 32 AF XY: 0.186 AC XY: 13857 AN XY: 74318

African (AFR) AF: 0.283 AC: 11721 AN: 41460

American (AMR) AF: 0.166 AC: 2537 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3468

East Asian (EAS) AF: 0.106 AC: 547 AN: 5180

South Asian (SAS) AF: 0.197 AC: 949 AN: 4820

European-Finnish (FIN) AF: 0.176 AC: 1858 AN: 10550

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8969 AN: 68006

Other (OTH) AF: 0.190 AC: 400 AN: 2110

Alfa AF: 0.131 Hom.: 772

Bravo AF: 0.184

Asia WGS AF: 0.206 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	12
DANN	Benign	0.59
Mutation Taster		=100/0	polymorphism (auto)

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: rs4359427; hg19: chr16-68202747;