rs504008

chr6-124629917-A-Cchr6-124629917-A-T

Variant summary

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

The NM_001040214.3(NKAIN2):c.274-28269A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,990 control chromosomes in the GnomAD database, including 32,201 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 0.63 (32201 hom., cov: 31)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKAIN2	NM_001040214.3	c.274-28269A>C		intron_variant		ENST00000368417.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN2	ENST00000368417.6	c.274-28269A>C		intron_variant		5	NM_001040214.3	P1
NKAIN2	ENST00000368416.5	c.274-28269A>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96002 AN: 151872 Hom.: 32203 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.632 AC: 96010 AN: 151990 Hom.: 32201 Cov.: 31 AF XY: 0.633 AC XY: 46978 AN XY: 74272

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.646

Alfa AF: 0.719 Hom.: 54654

Bravo AF: 0.612

Asia WGS AF: 0.637 AC: 2217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.53
Dann	Benign	0.58

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: rs504008; hg19: chr6-124951063;