rs12590407

Variant names:

• chr14-24365909-G-A
• rs12590407
• XR_007064085.1:n.758C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-24365909-G-A
• chr14-24365909-G-T

Variant summary

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

The XR_007064085.1(LOC124903291):​n.758C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,134 control chromosomes in the GnomAD database, including 35,124 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 0.68 (35124 hom., cov: 33)
• Consequence: LOC124903291 XR_007064085.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 21 publications found

Genes affected

LOC124903291 (HGNC:):

NFATC4 (HGNC:7778): (nuclear factor of activated T cells 4) This gene encodes a member of the nuclear factor of activated T cells (NFAT) protein family. The encoded protein is part of a 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 stimulation and an inducible nuclear component. NFAT proteins are activated by the calmodulin-dependent phosphatase, calcineurin. The encoded protein plays a role in the inducible expression of cytokine genes in T cells, especially in the induction of interleukin-2 and interleukin-4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440487.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFATC4	ENST00000440487.6	TSL:2	n.46+191G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102962 AN: 152016 Hom.: 35083 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.677 AC: 103063 AN: 152134 Hom.: 35124 Cov.: 33 AF XY: 0.679 AC XY: 50505 AN XY: 74384

African (AFR) AF: 0.628 AC: 26032 AN: 41464

American (AMR) AF: 0.597 AC: 9126 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2774 AN: 3472

East Asian (EAS) AF: 0.689 AC: 3555 AN: 5156

South Asian (SAS) AF: 0.692 AC: 3342 AN: 4830

European-Finnish (FIN) AF: 0.729 AC: 7733 AN: 10604

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48230 AN: 67992

Other (OTH) AF: 0.675 AC: 1429 AN: 2116

Alfa AF: 0.683 Hom.: 7828

Bravo AF: 0.661

Asia WGS AF: 0.716 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.6
DANN	Benign	0.67
PhyloP100		-0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12590407; hg19: chr14-24835115;