rs77490164

Variant names:

• chr6-124238586-C-T
• rs77490164
• NM_001040214.3:c.55-44419C>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.55-44419C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0436 in 152,202 control chromosomes in the GnomAD database, including 186 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 0.044 (186 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0565 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040214.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	NM_001040214.3	MANE Select	c.55-44419C>T		intron	N/A	NP_001035304.1	Q5VXU1-1
	NKAIN2	NM_001300737.2		c.52-44419C>T		intron	N/A	NP_001287666.1	Q5VXU1-3
	NKAIN2	NM_153355.5		c.55-44419C>T		intron	N/A	NP_699186.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	ENST00000368417.6	TSL:5 MANE Select	c.55-44419C>T		intron	N/A	ENSP00000357402.1	Q5VXU1-1
	NKAIN2	ENST00000368416.5	TSL:1	c.55-44419C>T		intron	N/A	ENSP00000357401.1	Q5VXU1-2
	NKAIN2	ENST00000476571.1	TSL:5	n.179-44419C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0436 AC: 6625 AN: 152084 Hom.: 186 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0436 AC: 6637 AN: 152202 Hom.: 186 Cov.: 32 AF XY: 0.0420 AC XY: 3127 AN XY: 74410

African (AFR) AF: 0.0305 AC: 1266 AN: 41534

American (AMR) AF: 0.0394 AC: 601 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0896 AC: 311 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.00269 AC: 13 AN: 4824

European-Finnish (FIN) AF: 0.0347 AC: 368 AN: 10604

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0580 AC: 3946 AN: 68016

Other (OTH) AF: 0.0449 AC: 95 AN: 2114

Alfa AF: 0.0564 Hom.: 39

Bravo AF: 0.0435

Asia WGS AF: 0.00491 AC: 17 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.27
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: rs77490164; hg19: chr6-124559732;