6-124370091-C-T

Variant names:

• chr6-124370091-C-T
• rs9491140
• NM_001040214.3:c.273+14744C>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+14744C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 150,580 control chromosomes in the GnomAD database, including 11,646 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 0.38 (11646 hom., cov: 27)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.715
• Publications: 15 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	NM_001040214.3	MANE Select	c.273+14744C>T		intron	N/A	NP_001035304.1	Q5VXU1-1
	NKAIN2	NM_001300737.2		c.270+14744C>T		intron	N/A	NP_001287666.1	Q5VXU1-3
	NKAIN2	NM_153355.5		c.273+14744C>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+14744C>T		intron	N/A	ENSP00000357402.1	Q5VXU1-1
	NKAIN2	ENST00000368416.5	TSL:1	c.273+14744C>T		intron	N/A	ENSP00000357401.1	Q5VXU1-2
	NKAIN2	ENST00000476571.1	TSL:5	n.397+14744C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57409 AN: 150464 Hom.: 11618 Cov.: 27

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.382 AC: 57503 AN: 150580 Hom.: 11646 Cov.: 27 AF XY: 0.379 AC XY: 27831 AN XY: 73378

African (AFR) AF: 0.530 AC: 21652 AN: 40846

American (AMR) AF: 0.410 AC: 6165 AN: 15036

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1166 AN: 3464

East Asian (EAS) AF: 0.244 AC: 1243 AN: 5104

South Asian (SAS) AF: 0.274 AC: 1301 AN: 4746

European-Finnish (FIN) AF: 0.335 AC: 3456 AN: 10316

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.315 AC: 21353 AN: 67770

Other (OTH) AF: 0.377 AC: 791 AN: 2096

Alfa AF: 0.342 Hom.: 25138

Bravo AF: 0.401

Asia WGS AF: 0.301 AC: 1046 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	12
DANN	Benign	0.54
PhyloP100		0.71
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: rs9491140; hg19: chr6-124691237;