NM_001040214.3:c.54+200828A>T

Variant names:

• chr6-124005082-A-T
• rs117780815
• NM_001040214.3:c.54+200828A>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.54+200828A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 151,882 control chromosomes in the GnomAD database, including 255 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 0.042 (255 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 9 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.114 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.54+200828A>T		intron	N/A	NP_001035304.1	Q5VXU1-1
	NKAIN2	NM_001300737.2		c.-13-116796A>T		intron	N/A	NP_001287666.1	Q5VXU1-3
	NKAIN2	NM_153355.5		c.54+200828A>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.54+200828A>T		intron	N/A	ENSP00000357402.1	Q5VXU1-1
	NKAIN2	ENST00000368416.5	TSL:1	c.54+200828A>T		intron	N/A	ENSP00000357401.1	Q5VXU1-2
	NKAIN2	ENST00000476571.1	TSL:5	n.115-116796A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 6302 AN: 151764 Hom.: 249 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0376

Gnomad EAS AF: 0.00795

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0381

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0417 AC: 6330 AN: 151882 Hom.: 255 Cov.: 32 AF XY: 0.0432 AC XY: 3212 AN XY: 74268

African (AFR) AF: 0.0107 AC: 443 AN: 41456

American (AMR) AF: 0.119 AC: 1815 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0376 AC: 130 AN: 3458

East Asian (EAS) AF: 0.00796 AC: 41 AN: 5148

South Asian (SAS) AF: 0.114 AC: 549 AN: 4798

European-Finnish (FIN) AF: 0.0472 AC: 498 AN: 10558

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0381 AC: 2585 AN: 67890

Other (OTH) AF: 0.0616 AC: 130 AN: 2112

Alfa AF: 0.0389 Hom.: 18

Bravo AF: 0.0474

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.25
PhyloP100		-0.55
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: rs117780815; hg19: chr6-124326227;