6-124481986-T-C

Variant names:

• chr6-124481986-T-C
• rs660197
• NM_001040214.3:c.273+126639T>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.273+126639T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,014 control chromosomes in the GnomAD database, including 46,211 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 0.78 (46211 hom., cov: 31)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.273+126639T>C		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+126639T>C		intron_variant	Intron 3 of 6	5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.273+126639T>C		intron_variant	Intron 3 of 3	1		ENSP00000357401.1

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118276 AN: 151898 Hom.: 46176 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.779 AC: 118369 AN: 152014 Hom.: 46211 Cov.: 31 AF XY: 0.777 AC XY: 57709 AN XY: 74286

African (AFR) AF: 0.815 AC: 33806 AN: 41458

American (AMR) AF: 0.730 AC: 11136 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3470

East Asian (EAS) AF: 0.771 AC: 3984 AN: 5164

South Asian (SAS) AF: 0.769 AC: 3706 AN: 4818

European-Finnish (FIN) AF: 0.776 AC: 8212 AN: 10576

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52595 AN: 67952

Other (OTH) AF: 0.736 AC: 1552 AN: 2108

Alfa AF: 0.786 Hom.: 5853

Bravo AF: 0.775

Asia WGS AF: 0.758 AC: 2634 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.50
PhyloP100		-1.9
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: rs660197; hg19: chr6-124803132;