6-124008733-G-C

Variant names:

• chr6-124008733-G-C
• rs1022106
• NM_001040214.3:c.54+204479G>C

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+204479G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,946 control chromosomes in the GnomAD database, including 17,832 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 0.48 (17832 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.54+204479G>C		intron_variant	Intron 1 of 6	ENST00000368417.6	NP_001035304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN2	ENST00000368417.6	c.54+204479G>C		intron_variant	Intron 1 of 6	5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.54+204479G>C		intron_variant	Intron 1 of 3	1		ENSP00000357401.1
NKAIN2	ENST00000476571.1	n.115-113145G>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73085 AN: 151828 Hom.: 17839 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.481 AC: 73112 AN: 151946 Hom.: 17832 Cov.: 32 AF XY: 0.487 AC XY: 36133 AN XY: 74246

African (AFR) AF: 0.438 AC: 18135 AN: 41408

American (AMR) AF: 0.394 AC: 6021 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1723 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2120 AN: 5142

South Asian (SAS) AF: 0.505 AC: 2431 AN: 4810

European-Finnish (FIN) AF: 0.564 AC: 5960 AN: 10572

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35058 AN: 67962

Other (OTH) AF: 0.490 AC: 1033 AN: 2108

Alfa AF: 0.373 Hom.: 1039

Bravo AF: 0.462

Asia WGS AF: 0.419 AC: 1459 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.7
DANN	Benign	0.31
PhyloP100		0.36
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: rs1022106; hg19: chr6-124329878;