chr6-124364036-A-G

Position:

• chr6-124364036-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040214.3(NKAIN2):​c.273+8689A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,606 control chromosomes in the GnomAD database, including 15,693 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 0.45 (15693 hom., cov: 31)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

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]

NKAIN2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.273+8689A>G		intron_variant		ENST00000368417.6	NP_001035304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NKAIN2	ENST00000368417.6	c.273+8689A>G		intron_variant		5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.273+8689A>G		intron_variant		1		ENSP00000357401.1
NKAIN2	ENST00000476571.1	n.397+8689A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68706 AN: 151484 Hom.: 15683 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.454 AC: 68754 AN: 151606 Hom.: 15693 Cov.: 31 AF XY: 0.459 AC XY: 33989 AN XY: 74064

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.432

Alfa AF: 0.452 Hom.: 23031

Bravo AF: 0.444

Asia WGS AF: 0.504 AC: 1726 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.34

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

Publications

LitVar

Other links and lift over

dbSNP: rs1407529; hg19: chr6-124685182;