6-124205531-G-T

Variant names:

• chr6-124205531-G-T
• rs699376
• NM_001040214.3:c.55-77474G>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.55-77474G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,400 control chromosomes in the GnomAD database, including 36,197 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 0.69 (36197 hom., cov: 31)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKAIN2	NM_001040214.3	c.55-77474G>T		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.55-77474G>T		intron_variant	Intron 1 of 6	5	NM_001040214.3	ENSP00000357402.1
NKAIN2	ENST00000368416.5	c.55-77474G>T		intron_variant	Intron 1 of 3	1		ENSP00000357401.1
NKAIN2	ENST00000476571.1	n.179-77474G>T		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104333 AN: 151282 Hom.: 36174 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.690 AC: 104402 AN: 151400 Hom.: 36197 Cov.: 31 AF XY: 0.692 AC XY: 51215 AN XY: 73960

African (AFR) AF: 0.637 AC: 26339 AN: 41334

American (AMR) AF: 0.670 AC: 10143 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2114 AN: 3456

East Asian (EAS) AF: 0.644 AC: 3302 AN: 5130

South Asian (SAS) AF: 0.749 AC: 3607 AN: 4814

European-Finnish (FIN) AF: 0.756 AC: 7963 AN: 10530

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48566 AN: 67698

Other (OTH) AF: 0.681 AC: 1424 AN: 2092

Alfa AF: 0.695 Hom.: 6388

Bravo AF: 0.682

Asia WGS AF: 0.687 AC: 2386 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.52
PhyloP100		-0.28
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: rs699376; hg19: chr6-124526676;