rs870583

Variant names:

• chr6-124734383-G-A
• rs870583
• NM_001040214.3:c.475-56956G>A

Variant summary

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

The NM_001040214.3(NKAIN2):​c.475-56956G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 151,596 control chromosomes in the GnomAD database, including 1,521 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 0.12 (1521 hom., cov: 31)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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:50866): (RNF217 antisense RNA 1 (head to head))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.475-56956G>A		intron_variant	Intron 4 of 6	ENST00000368417.6	NP_001035304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN2	ENST00000368417.6	c.475-56956G>A		intron_variant	Intron 4 of 6	5	NM_001040214.3	ENSP00000357402.1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18825 AN: 151478 Hom.: 1514 Cov.: 31

Gnomad AFR AF: 0.0702

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.124 AC: 18842 AN: 151596 Hom.: 1521 Cov.: 31 AF XY: 0.131 AC XY: 9712 AN XY: 74032

Gnomad4 AFR AF: 0.0701

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.141

Alfa AF: 0.118 Hom.: 1437

Bravo AF: 0.126

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.79

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: rs870583; hg19: chr6-125055529;