rs870583

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040214.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	NM_001040214.3	MANE Select	c.475-56956G>A		intron	N/A	NP_001035304.1
	NKAIN2	NM_001300737.2		c.472-56956G>A		intron	N/A	NP_001287666.1
	NKAIN2	NM_153355.5		c.274-56956G>A		intron	N/A	NP_699186.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	ENST00000368417.6	TSL:5 MANE Select	c.475-56956G>A		intron	N/A	ENSP00000357402.1
	RNF217-AS1	ENST00000655205.1		n.920-51361C>T		intron	N/A
	RNF217-AS1	ENST00000658682.1		n.824+10013C>T		intron	N/A

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

African (AFR) AF: 0.0701 AC: 2904 AN: 41426

American (AMR) AF: 0.209 AC: 3181 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3462

East Asian (EAS) AF: 0.346 AC: 1764 AN: 5102

South Asian (SAS) AF: 0.168 AC: 810 AN: 4808

European-Finnish (FIN) AF: 0.168 AC: 1771 AN: 10542

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7501 AN: 67752

Other (OTH) AF: 0.141 AC: 297 AN: 2108

Alfa AF: 0.118 Hom.: 1861

Bravo AF: 0.126

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.79
PhyloP100		-0.099
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: rs870583; hg19: chr6-125055529;