6-123874662-A-T

Variant names:

• chr6-123874662-A-T
• rs9320964
• NM_001040214.3:c.54+70408A>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+70408A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,942 control chromosomes in the GnomAD database, including 9,624 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 0.35 (9624 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.54+70408A>T		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+70408A>T		intron_variant	Intron 1 of 6	5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.54+70408A>T		intron_variant	Intron 1 of 3	1		ENSP00000357401.1
NKAIN2	ENST00000476571.1	n.114+70408A>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53289 AN: 151824 Hom.: 9617 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.351 AC: 53329 AN: 151942 Hom.: 9624 Cov.: 32 AF XY: 0.351 AC XY: 26081 AN XY: 74272

African (AFR) AF: 0.396 AC: 16431 AN: 41456

American (AMR) AF: 0.320 AC: 4878 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1041 AN: 5174

South Asian (SAS) AF: 0.205 AC: 988 AN: 4824

European-Finnish (FIN) AF: 0.407 AC: 4277 AN: 10514

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23578 AN: 67954

Other (OTH) AF: 0.329 AC: 693 AN: 2108

Alfa AF: 0.356 Hom.: 1228

Bravo AF: 0.346

Asia WGS AF: 0.198 AC: 686 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.50
PhyloP100		-1.3
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: rs9320964; hg19: chr6-124195807; COSMIC: COSV63648994;