rs504008

Variant names:

• chr6-124629917-A-C
• rs504008
• NM_001040214.3:c.274-28269A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-124629917-A-C
• chr6-124629917-A-G
• chr6-124629917-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.85).
• 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 rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.274-28269A>C		intron_variant	Intron 3 of 6	ENST00000368417.6	NP_001035304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKAIN2	ENST00000368417.6	c.274-28269A>C		intron_variant	Intron 3 of 6	5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.274-28269A>C		intron_variant	Intron 3 of 3	1		ENSP00000357401.1

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

African (AFR) AF: 0.391 AC: 16203 AN: 41432

American (AMR) AF: 0.655 AC: 9998 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2662 AN: 3472

East Asian (EAS) AF: 0.621 AC: 3191 AN: 5140

South Asian (SAS) AF: 0.662 AC: 3195 AN: 4826

European-Finnish (FIN) AF: 0.749 AC: 7916 AN: 10566

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50800 AN: 67986

Other (OTH) AF: 0.646 AC: 1363 AN: 2110

Alfa AF: 0.705 Hom.: 117898

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
PhyloP100		-0.34
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: rs504008; hg19: chr6-124951063;