NM_173165.3:c.1402-6612G>A

Variant names:

• chr16-68151257-G-A
• rs7193701
• NM_173165.3:c.1402-6612G>A

Variant summary

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

The NM_173165.3(NFATC3):​c.1402-6612G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,696 control chromosomes in the GnomAD database, including 4,132 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 0.22 (4132 hom., cov: 31)
• Consequence: NFATC3 NM_173165.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 18 publications found

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=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFATC3	NM_173165.3	c.1402-6612G>A		intron_variant	Intron 3 of 9	ENST00000346183.8	NP_775188.1
NFATC3	NM_004555.4	c.1402-6612G>A		intron_variant	Intron 3 of 10		NP_004546.1
NFATC3	NM_173163.3	c.1402-6612G>A		intron_variant	Intron 3 of 10		NP_775186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFATC3	ENST00000346183.8	c.1402-6612G>A		intron_variant	Intron 3 of 9	1	NM_173165.3	ENSP00000300659.5

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32866 AN: 151588 Hom.: 4112 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.217 AC: 32931 AN: 151696 Hom.: 4132 Cov.: 31 AF XY: 0.218 AC XY: 16163 AN XY: 74074

African (AFR) AF: 0.334 AC: 13814 AN: 41344

American (AMR) AF: 0.199 AC: 3031 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3466

East Asian (EAS) AF: 0.107 AC: 552 AN: 5168

South Asian (SAS) AF: 0.218 AC: 1047 AN: 4794

European-Finnish (FIN) AF: 0.185 AC: 1934 AN: 10460

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.161 AC: 10946 AN: 67926

Other (OTH) AF: 0.232 AC: 488 AN: 2100

Alfa AF: 0.183 Hom.: 8112

Bravo AF: 0.222

Asia WGS AF: 0.221 AC: 766 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	10
DANN	Benign	0.86
PhyloP100		-0.54
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

Other links and lift over

dbSNP: rs7193701; hg19: chr16-68185160;