6-124121141-C-T

Variant names:

• chr6-124121141-C-T
• rs594664
• NM_001040214.3:c.55-161864C>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.55-161864C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,700 control chromosomes in the GnomAD database, including 11,109 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 0.38 (11109 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) 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.55-161864C>T		intron	N/A	NP_001035304.1
	NKAIN2	NM_001300737.2		c.-13-737C>T		intron	N/A	NP_001287666.1
	NKAIN2	NM_153355.5		c.55-161864C>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.55-161864C>T		intron	N/A	ENSP00000357402.1
	NKAIN2	ENST00000368416.5	TSL:1	c.55-161864C>T		intron	N/A	ENSP00000357401.1
	NKAIN2	ENST00000476571.1	TSL:5	n.115-737C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.376 AC: 56954 AN: 151582 Hom.: 11112 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.375 AC: 56938 AN: 151700 Hom.: 11109 Cov.: 32 AF XY: 0.377 AC XY: 27950 AN XY: 74094

African (AFR) AF: 0.289 AC: 11955 AN: 41380

American (AMR) AF: 0.281 AC: 4280 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1392 AN: 3464

East Asian (EAS) AF: 0.294 AC: 1507 AN: 5132

South Asian (SAS) AF: 0.436 AC: 2100 AN: 4814

European-Finnish (FIN) AF: 0.495 AC: 5205 AN: 10524

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.432 AC: 29335 AN: 67848

Other (OTH) AF: 0.363 AC: 763 AN: 2102

Alfa AF: 0.408 Hom.: 55319

Bravo AF: 0.351

Asia WGS AF: 0.328 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.81
PhyloP100		0.14
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: rs594664; hg19: chr6-124442286; COSMIC: COSV63649357; COSMIC: COSV63649357;