rs9889219

Variant names:

• chr16-69687512-G-A
• rs9889219
• NM_138713.4:c.1774+2542G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-69687512-G-A
• chr16-69687512-G-T

Variant summary

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

The NM_138713.4(NFAT5):​c.1774+2542G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 150,444 control chromosomes in the GnomAD database, including 6,877 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 0.29 (6877 hom., cov: 29)
• Consequence: NFAT5 NM_138713.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 12 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFAT5	NM_138713.4	c.1774+2542G>A		intron_variant	Intron 11 of 14	ENST00000349945.7	NP_619727.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFAT5	ENST00000349945.7	c.1774+2542G>A		intron_variant	Intron 11 of 14	1	NM_138713.4	ENSP00000338806.3

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43384 AN: 150348 Hom.: 6848 Cov.: 29

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.300

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.289 AC: 43458 AN: 150444 Hom.: 6877 Cov.: 29 AF XY: 0.287 AC XY: 21054 AN XY: 73374

African (AFR) AF: 0.412 AC: 16869 AN: 40910

American (AMR) AF: 0.173 AC: 2617 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1930 AN: 5074

South Asian (SAS) AF: 0.227 AC: 1081 AN: 4766

European-Finnish (FIN) AF: 0.243 AC: 2440 AN: 10046

Middle Eastern (MID) AF: 0.303 AC: 86 AN: 284

European-Non Finnish (NFE) AF: 0.245 AC: 16611 AN: 67802

Other (OTH) AF: 0.271 AC: 566 AN: 2090

Alfa AF: 0.261 Hom.: 17448

Bravo AF: 0.289

Asia WGS AF: 0.298 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		0.28
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: rs9889219; hg19: chr16-69721415;