6-124239537-A-C

Variant names:

• chr6-124239537-A-C
• rs1089567
• NM_001040214.3:c.55-43468A>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.55-43468A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,064 control chromosomes in the GnomAD database, including 46,044 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 (46044 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.55-43468A>C		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.55-43468A>C		intron_variant	Intron 1 of 6	5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.55-43468A>C		intron_variant	Intron 1 of 3	1		ENSP00000357401.1
NKAIN2	ENST00000476571.1	n.179-43468A>C		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118032 AN: 151946 Hom.: 46014 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.777 AC: 118117 AN: 152064 Hom.: 46044 Cov.: 32 AF XY: 0.778 AC XY: 57790 AN XY: 74320

African (AFR) AF: 0.754 AC: 31275 AN: 41490

American (AMR) AF: 0.739 AC: 11278 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2503 AN: 3468

East Asian (EAS) AF: 0.734 AC: 3784 AN: 5158

South Asian (SAS) AF: 0.851 AC: 4105 AN: 4826

European-Finnish (FIN) AF: 0.791 AC: 8366 AN: 10580

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54096 AN: 67978

Other (OTH) AF: 0.771 AC: 1626 AN: 2108

Alfa AF: 0.778 Hom.: 5713

Bravo AF: 0.773

Asia WGS AF: 0.776 AC: 2699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.83
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: rs1089567; hg19: chr6-124560683;