NM_001040214.3:c.273+16524G>A

Variant names:

• chr6-124371871-G-A
• rs9491142
• NM_001040214.3:c.273+16524G>A

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+16524G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,662 control chromosomes in the GnomAD database, including 11,829 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 (11829 hom., cov: 31)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• Publications: 1 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.273+16524G>A		intron_variant	Intron 3 of 6	ENST00000368417.6	NP_001035304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN2	ENST00000368417.6	c.273+16524G>A		intron_variant	Intron 3 of 6	5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.273+16524G>A		intron_variant	Intron 3 of 3	1		ENSP00000357401.1
NKAIN2	ENST00000476571.1	n.397+16524G>A		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58019 AN: 151544 Hom.: 11804 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.383 AC: 58110 AN: 151662 Hom.: 11829 Cov.: 31 AF XY: 0.381 AC XY: 28203 AN XY: 74104

African (AFR) AF: 0.535 AC: 22135 AN: 41350

American (AMR) AF: 0.408 AC: 6214 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1164 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1216 AN: 5122

South Asian (SAS) AF: 0.278 AC: 1337 AN: 4808

European-Finnish (FIN) AF: 0.334 AC: 3512 AN: 10504

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21367 AN: 67876

Other (OTH) AF: 0.373 AC: 786 AN: 2106

Alfa AF: 0.330 Hom.: 5074

Bravo AF: 0.402

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.8
DANN	Benign	0.66
PhyloP100		0.48
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: rs9491142; hg19: chr6-124693017;