rs12204812

chr6-124360357-C-Achr6-124360357-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040214.3(NKAIN2):c.273+5010C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,934 control chromosomes in the GnomAD database, including 10,022 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 0.36 (10022 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKAIN2	NM_001040214.3	c.273+5010C>A		intron_variant		ENST00000368417.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN2	ENST00000368417.6	c.273+5010C>A		intron_variant		5	NM_001040214.3	P1
NKAIN2	ENST00000368416.5	c.273+5010C>A		intron_variant		1
NKAIN2	ENST00000476571.1	n.397+5010C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54226 AN: 151816 Hom.: 9995 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.357 AC: 54313 AN: 151934 Hom.: 10022 Cov.: 32 AF XY: 0.356 AC XY: 26408 AN XY: 74258

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.360

Alfa AF: 0.313 Hom.: 13664

Bravo AF: 0.373

Asia WGS AF: 0.288 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.055
Dann	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs12204812; hg19: chr6-124681503;