16-69692979-CAG-AGA

Variant names:

• chr16-69692979-CAG-AGA
• NM_138713.4:c.3154_3156delCAGinsAGA
• NFAT5 p.Gln1052Arg

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_138713.4(NFAT5):​c.3154_3156delCAGinsAGA​(p.Gln1052Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: NFAT5 NM_138713.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.87
• Publications: 0 publications found

Genes affected

NFAT5 (HGNC:7774): (nuclear factor of activated T cells 5) The product of this gene is a member of the nuclear factors of activated T cells family of transcription factors. Proteins belonging to this family play a central role in inducible gene transcription during the immune response. This protein regulates gene expression induced by osmotic stress in mammalian cells. Unlike monomeric members of this protein family, this protein exists as a homodimer and forms stable dimers with DNA elements. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138713.4. 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
	NFAT5	NM_138713.4	MANE Select	c.3154_3156delCAGinsAGA	p.Gln1052Arg	missense	N/A	NP_619727.2	O94916-5
	NFAT5	NM_001113178.3		c.3151_3153delCAGinsAGA	p.Gln1051Arg	missense	N/A	NP_001106649.1	O94916-4
	NFAT5	NM_006599.4		c.3100_3102delCAGinsAGA	p.Gln1034Arg	missense	N/A	NP_006590.1	O94916-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFAT5	ENST00000349945.7	TSL:1 MANE Select	c.3154_3156delCAGinsAGA	p.Gln1052Arg	missense	N/A	ENSP00000338806.3	O94916-5
	NFAT5	ENST00000567239.5	TSL:1	c.3151_3153delCAGinsAGA	p.Gln1051Arg	missense	N/A	ENSP00000457593.1	O94916-4
	NFAT5	ENST00000354436.6	TSL:1	c.3100_3102delCAGinsAGA	p.Gln1034Arg	missense	N/A	ENSP00000346420.2	O94916-1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr16-69726882;