rs2418736

Variant names:

• chr16-68120959-G-A
• rs2418736
• NM_173165.3:c.104-1028G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-68120959-G-A
• chr16-68120959-G-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.104-1028G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,758 control chromosomes in the GnomAD database, including 7,379 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 0.28 (7379 hom., cov: 31)
• Consequence: NFATC3 NM_173165.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 20 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]

ENSG00000261864 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFATC3	NM_173165.3	c.104-1028G>A		intron_variant	Intron 1 of 9	ENST00000346183.8	NP_775188.1
NFATC3	NM_004555.4	c.104-1028G>A		intron_variant	Intron 1 of 10		NP_004546.1
NFATC3	NM_173163.3	c.104-1028G>A		intron_variant	Intron 1 of 10		NP_775186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFATC3	ENST00000346183.8	c.104-1028G>A		intron_variant	Intron 1 of 9	1	NM_173165.3	ENSP00000300659.5

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42070 AN: 151640 Hom.: 7348 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.278 AC: 42154 AN: 151758 Hom.: 7379 Cov.: 31 AF XY: 0.278 AC XY: 20593 AN XY: 74120

African (AFR) AF: 0.497 AC: 20555 AN: 41362

American (AMR) AF: 0.233 AC: 3559 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 813 AN: 3468

East Asian (EAS) AF: 0.108 AC: 562 AN: 5186

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4822

European-Finnish (FIN) AF: 0.208 AC: 2169 AN: 10424

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12332 AN: 67936

Other (OTH) AF: 0.275 AC: 578 AN: 2102

Alfa AF: 0.213 Hom.: 6519

Bravo AF: 0.284

Asia WGS AF: 0.253 AC: 881 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.72
PhyloP100		-0.91
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: rs2418736; hg19: chr16-68154862;