6-124440303-C-T

Variant names:

• chr6-124440303-C-T
• rs590944
• NM_001040214.3:c.273+84956C>T

Variant summary

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

The NM_001040214.3(NKAIN2):​c.273+84956C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,870 control chromosomes in the GnomAD database, including 7,646 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 0.30 (7646 hom., cov: 31)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	NM_001040214.3	MANE Select	c.273+84956C>T		intron	N/A	NP_001035304.1	Q5VXU1-1
	NKAIN2	NM_001300737.2		c.270+84956C>T		intron	N/A	NP_001287666.1	Q5VXU1-3
	NKAIN2	NM_153355.5		c.273+84956C>T		intron	N/A	NP_699186.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	ENST00000368417.6	TSL:5 MANE Select	c.273+84956C>T		intron	N/A	ENSP00000357402.1	Q5VXU1-1
	NKAIN2	ENST00000368416.5	TSL:1	c.273+84956C>T		intron	N/A	ENSP00000357401.1	Q5VXU1-2

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46149 AN: 151752 Hom.: 7618 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.304 AC: 46224 AN: 151870 Hom.: 7646 Cov.: 31 AF XY: 0.298 AC XY: 22113 AN XY: 74226

African (AFR) AF: 0.433 AC: 17937 AN: 41406

American (AMR) AF: 0.238 AC: 3635 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 789 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1241 AN: 5122

South Asian (SAS) AF: 0.193 AC: 930 AN: 4810

European-Finnish (FIN) AF: 0.260 AC: 2754 AN: 10572

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17908 AN: 67930

Other (OTH) AF: 0.279 AC: 588 AN: 2108

Alfa AF: 0.169 Hom.: 317

Bravo AF: 0.310

Asia WGS AF: 0.260 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		-0.34
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: rs590944; hg19: chr6-124761449; COSMIC: COSV63650107;