rs4466264

Variant names:

• chr6-124744140-T-A
• rs4466264
• NM_001040214.3:c.475-47199T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-124744140-T-A
• chr6-124744140-T-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.475-47199T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,688 control chromosomes in the GnomAD database, including 11,410 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 0.38 (11410 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 2 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]

RNF217-AS1 (HGNC:50866): (RNF217 antisense RNA 1 (head to head))

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.475-47199T>A		intron_variant	Intron 4 of 6	ENST00000368417.6	NP_001035304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN2	ENST00000368417.6	c.475-47199T>A		intron_variant	Intron 4 of 6	5	NM_001040214.3	ENSP00000357402.1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58302 AN: 151570 Hom.: 11405 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.385 AC: 58336 AN: 151688 Hom.: 11410 Cov.: 32 AF XY: 0.391 AC XY: 28960 AN XY: 74118

African (AFR) AF: 0.370 AC: 15334 AN: 41400

American (AMR) AF: 0.453 AC: 6893 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1153 AN: 3462

East Asian (EAS) AF: 0.332 AC: 1700 AN: 5120

South Asian (SAS) AF: 0.371 AC: 1787 AN: 4816

European-Finnish (FIN) AF: 0.489 AC: 5162 AN: 10566

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25127 AN: 67800

Other (OTH) AF: 0.380 AC: 800 AN: 2108

Alfa AF: 0.378 Hom.: 1349

Bravo AF: 0.380

Asia WGS AF: 0.345 AC: 1199 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.66
PhyloP100		0.23
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: rs4466264; hg19: chr6-125065286;