chr6-124364036-A-G

Variant names:

• chr6-124364036-A-G
• rs1407529
• NM_001040214.3:c.273+8689A>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.273+8689A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,606 control chromosomes in the GnomAD database, including 15,693 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 0.45 (15693 hom., cov: 31)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 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.273+8689A>G		intron	N/A	NP_001035304.1
	NKAIN2	NM_001300737.2		c.270+8689A>G		intron	N/A	NP_001287666.1
	NKAIN2	NM_153355.5		c.273+8689A>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.273+8689A>G		intron	N/A	ENSP00000357402.1
	NKAIN2	ENST00000368416.5	TSL:1	c.273+8689A>G		intron	N/A	ENSP00000357401.1
	NKAIN2	ENST00000476571.1	TSL:5	n.397+8689A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68706 AN: 151484 Hom.: 15683 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.454 AC: 68754 AN: 151606 Hom.: 15693 Cov.: 31 AF XY: 0.459 AC XY: 33989 AN XY: 74064

African (AFR) AF: 0.442 AC: 18312 AN: 41392

American (AMR) AF: 0.444 AC: 6765 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1324 AN: 3472

East Asian (EAS) AF: 0.491 AC: 2530 AN: 5148

South Asian (SAS) AF: 0.541 AC: 2599 AN: 4802

European-Finnish (FIN) AF: 0.496 AC: 5173 AN: 10436

Middle Eastern (MID) AF: 0.428 AC: 124 AN: 290

European-Non Finnish (NFE) AF: 0.453 AC: 30706 AN: 67810

Other (OTH) AF: 0.432 AC: 907 AN: 2100

Alfa AF: 0.452 Hom.: 48008

Bravo AF: 0.444

Asia WGS AF: 0.504 AC: 1726 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.34
PhyloP100		0.10
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: rs1407529; hg19: chr6-124685182;