6-124387343-A-G

Variant names:

• chr6-124387343-A-G
• rs332610
• NM_001040214.3:c.273+31996A>G

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+31996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,232 control chromosomes in the GnomAD database, including 25,364 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 0.58 (25364 hom., cov: 29)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 0 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.273+31996A>G		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+31996A>G		intron_variant	Intron 3 of 6	5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.273+31996A>G		intron_variant	Intron 3 of 3	1		ENSP00000357401.1
NKAIN2	ENST00000476571.1	n.398-3390A>G		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87401 AN: 151114 Hom.: 25355 Cov.: 29

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.578 AC: 87443 AN: 151232 Hom.: 25364 Cov.: 29 AF XY: 0.585 AC XY: 43180 AN XY: 73868

African (AFR) AF: 0.574 AC: 23644 AN: 41192

American (AMR) AF: 0.543 AC: 8257 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1591 AN: 3466

East Asian (EAS) AF: 0.575 AC: 2943 AN: 5118

South Asian (SAS) AF: 0.665 AC: 3189 AN: 4794

European-Finnish (FIN) AF: 0.654 AC: 6794 AN: 10388

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39236 AN: 67764

Other (OTH) AF: 0.537 AC: 1128 AN: 2102

Alfa AF: 0.586 Hom.: 3137

Bravo AF: 0.564

Asia WGS AF: 0.625 AC: 2173 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.52
DANN	Benign	0.81
PhyloP100		-1.4
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: rs332610; hg19: chr6-124708489;