chr6-124202310-C-A

Variant names:

• chr6-124202310-C-A
• rs2056561
• NM_001040214.3:c.55-80695C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040214.3(NKAIN2):​c.55-80695C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 151,982 control chromosomes in the GnomAD database, including 489 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 0.058 (489 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.55-80695C>A		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.55-80695C>A		intron_variant	Intron 1 of 6	5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.55-80695C>A		intron_variant	Intron 1 of 3	1		ENSP00000357401.1
NKAIN2	ENST00000476571.1	n.178+80369C>A		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0577 AC: 8767 AN: 151864 Hom.: 484 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0416

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.0447

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0578 AC: 8787 AN: 151982 Hom.: 489 Cov.: 32 AF XY: 0.0605 AC XY: 4492 AN XY: 74288

African (AFR) AF: 0.125 AC: 5173 AN: 41488

American (AMR) AF: 0.100 AC: 1526 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0416 AC: 144 AN: 3464

East Asian (EAS) AF: 0.0733 AC: 379 AN: 5168

South Asian (SAS) AF: 0.0450 AC: 217 AN: 4824

European-Finnish (FIN) AF: 0.0179 AC: 190 AN: 10606

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0155 AC: 1054 AN: 67900

Other (OTH) AF: 0.0455 AC: 96 AN: 2110

Alfa AF: 0.0291 Hom.: 64

Bravo AF: 0.0659

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.79
PhyloP100		-0.20
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: rs2056561; hg19: chr6-124523455;