chr6-124750876-A-G

Variant names:

• chr6-124750876-A-G
• rs9398764
• NM_001040214.3:c.475-40463A>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.475-40463A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,674 control chromosomes in the GnomAD database, including 9,270 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 0.34 (9270 hom., cov: 31)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• 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]

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.374 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	NM_001040214.3	MANE Select	c.475-40463A>G		intron	N/A	NP_001035304.1
	NKAIN2	NM_001300737.2		c.472-40463A>G		intron	N/A	NP_001287666.1
	NKAIN2	NM_153355.5		c.274-40463A>G		intron	N/A	NP_699186.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NKAIN2	ENST00000368417.6	TSL:5 MANE Select	c.475-40463A>G		intron	N/A	ENSP00000357402.1
	RNF217-AS1	ENST00000655205.1		n.919+35584T>C		intron	N/A
	RNF217-AS1	ENST00000658682.1		n.748-6404T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52115 AN: 151556 Hom.: 9262 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.344 AC: 52140 AN: 151674 Hom.: 9270 Cov.: 31 AF XY: 0.349 AC XY: 25874 AN XY: 74124

African (AFR) AF: 0.278 AC: 11503 AN: 41384

American (AMR) AF: 0.382 AC: 5819 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3466

East Asian (EAS) AF: 0.285 AC: 1446 AN: 5068

South Asian (SAS) AF: 0.373 AC: 1791 AN: 4806

European-Finnish (FIN) AF: 0.447 AC: 4724 AN: 10564

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24776 AN: 67858

Other (OTH) AF: 0.335 AC: 704 AN: 2100

Alfa AF: 0.355 Hom.: 1419

Bravo AF: 0.332

Asia WGS AF: 0.319 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		-0.36
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: rs9398764; hg19: chr6-125072022;