rs6917824

Variant names:

• chr6-124021518-A-G
• rs6917824
• NM_001040214.3:c.54+217264A>G

Variant summary

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

The NM_001040214.3(NKAIN2):​c.54+217264A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,814 control chromosomes in the GnomAD database, including 4,863 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 0.23 (4863 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 7 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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.54+217264A>G		intron	N/A	NP_001035304.1
	NKAIN2	NM_001300737.2		c.-13-100360A>G		intron	N/A	NP_001287666.1
	NKAIN2	NM_153355.5		c.54+217264A>G		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.54+217264A>G		intron	N/A	ENSP00000357402.1
	NKAIN2	ENST00000368416.5	TSL:1	c.54+217264A>G		intron	N/A	ENSP00000357401.1
	NKAIN2	ENST00000476571.1	TSL:5	n.115-100360A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34208 AN: 151702 Hom.: 4848 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.00734

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0965

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.226 AC: 34271 AN: 151814 Hom.: 4863 Cov.: 32 AF XY: 0.222 AC XY: 16483 AN XY: 74222

African (AFR) AF: 0.396 AC: 16374 AN: 41392

American (AMR) AF: 0.248 AC: 3769 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3464

East Asian (EAS) AF: 0.00716 AC: 37 AN: 5168

South Asian (SAS) AF: 0.191 AC: 918 AN: 4818

European-Finnish (FIN) AF: 0.0965 AC: 1018 AN: 10552

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.156 AC: 10577 AN: 67898

Other (OTH) AF: 0.240 AC: 505 AN: 2100

Alfa AF: 0.201 Hom.: 2361

Bravo AF: 0.249

Asia WGS AF: 0.141 AC: 483 AN: 3412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.85
PhyloP100		1.4
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: rs6917824; hg19: chr6-124342663;