NM_138713.4:c.127+4010G>A

Variant names:

• chr16-69572558-G-A
• rs2161630
• NM_138713.4:c.127+4010G>A

Variant summary

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

The NM_138713.4(NFAT5):​c.127+4010G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,832 control chromosomes in the GnomAD database, including 24,003 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 0.55 (24003 hom., cov: 32)
• Consequence: NFAT5 NM_138713.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 7 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFAT5	NM_138713.4	c.127+4010G>A		intron_variant	Intron 2 of 14	ENST00000349945.7	NP_619727.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFAT5	ENST00000349945.7	c.127+4010G>A		intron_variant	Intron 2 of 14	1	NM_138713.4	ENSP00000338806.3

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82640 AN: 151714 Hom.: 23953 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.545 AC: 82761 AN: 151832 Hom.: 24003 Cov.: 32 AF XY: 0.548 AC XY: 40629 AN XY: 74168

African (AFR) AF: 0.734 AC: 30397 AN: 41412

American (AMR) AF: 0.522 AC: 7958 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1663 AN: 3464

East Asian (EAS) AF: 0.812 AC: 4203 AN: 5174

South Asian (SAS) AF: 0.555 AC: 2673 AN: 4816

European-Finnish (FIN) AF: 0.434 AC: 4545 AN: 10472

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29636 AN: 67924

Other (OTH) AF: 0.531 AC: 1121 AN: 2110

Alfa AF: 0.466 Hom.: 8542

Bravo AF: 0.561

Asia WGS AF: 0.627 AC: 2156 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.3
DANN	Benign	0.45
PhyloP100		1.6
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: rs2161630; hg19: chr16-69606461;