chr6-124008168-G-A

Variant names:

• chr6-124008168-G-A
• rs1510295
• NM_001040214.3:c.54+203914G>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.54+203914G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,200 control chromosomes in the GnomAD database, including 58,503 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 0.88 (58503 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.54+203914G>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.54+203914G>A		intron_variant	Intron 1 of 6	5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.54+203914G>A		intron_variant	Intron 1 of 3	1		ENSP00000357401.1
NKAIN2	ENST00000476571.1	n.115-113710G>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133130 AN: 152082 Hom.: 58473 Cov.: 32

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.875 AC: 133213 AN: 152200 Hom.: 58503 Cov.: 32 AF XY: 0.875 AC XY: 65086 AN XY: 74402

African (AFR) AF: 0.918 AC: 38153 AN: 41546

American (AMR) AF: 0.810 AC: 12368 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2981 AN: 3472

East Asian (EAS) AF: 0.981 AC: 5059 AN: 5156

South Asian (SAS) AF: 0.849 AC: 4095 AN: 4826

European-Finnish (FIN) AF: 0.856 AC: 9059 AN: 10588

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58790 AN: 68020

Other (OTH) AF: 0.858 AC: 1813 AN: 2114

Alfa AF: 0.867 Hom.: 174197

Bravo AF: 0.870

Asia WGS AF: 0.902 AC: 3135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.73
DANN	Benign	0.79
PhyloP100		-0.018
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: rs1510295; hg19: chr6-124329313;