rs10499129

chr6-124613061-A-G

Variant summary

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

The NM_001040214.3(NKAIN2):c.274-45125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,138 control chromosomes in the GnomAD database, including 1,456 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 0.13 (1456 hom., cov: 32)
• Consequence: NKAIN2 NM_001040214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NKAIN2	NM_001040214.3	c.274-45125A>G		intron_variant		ENST00000368417.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NKAIN2	ENST00000368417.6	c.274-45125A>G		intron_variant		5	NM_001040214.3	P1
NKAIN2	ENST00000368416.5	c.274-45125A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20076 AN: 152022 Hom.: 1452 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.132 AC: 20094 AN: 152138 Hom.: 1456 Cov.: 32 AF XY: 0.135 AC XY: 10036 AN XY: 74384

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.148

Alfa AF: 0.112 Hom.: 1300

Bravo AF: 0.133

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.011
Dann	Benign	0.28

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: rs10499129; hg19: chr6-124934207; COSMIC: COSV63686991;