rs9398764

Positions:

• chr6-124750876-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040214.3(NKAIN2):​c.475-40463A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,674 control chromosomes in the GnomAD database, including 9,270 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 0.34 (9270 hom., cov: 31)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

Genes affected

NKAIN2 (HGNC:16443): (sodium/potassium transporting ATPase interacting 2) This gene encodes a transmembrane protein that interacts with the beta subunit of a sodium/potassium-transporting ATPase. A chromosomal translocation involving this gene is a cause of lymphoma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]

RNF217-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.475-40463A>G		intron_variant		ENST00000368417.6	NP_001035304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NKAIN2	ENST00000368417.6	c.475-40463A>G		intron_variant		5	NM_001040214.3	ENSP00000357402.1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52115 AN: 151556 Hom.: 9262 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.344 AC: 52140 AN: 151674 Hom.: 9270 Cov.: 31 AF XY: 0.349 AC XY: 25874 AN XY: 74124

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.335

Alfa AF: 0.355 Hom.: 1419

Bravo AF: 0.332

Asia WGS AF: 0.319 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs9398764; hg19: chr6-125072022;