6-124361442-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001040214.3(NKAIN2):​c.273+6095A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 151,980 control chromosomes in the GnomAD database, including 56,520 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 0.86 ( 56520 hom., cov: 31)

Consequence

NKAIN2
NM_001040214.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.665
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NKAIN2NM_001040214.3 linkc.273+6095A>G intron_variant Intron 3 of 6 ENST00000368417.6 NP_001035304.1 Q5VXU1-1B3KNZ0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NKAIN2ENST00000368417.6 linkc.273+6095A>G intron_variant Intron 3 of 6 5 NM_001040214.3 ENSP00000357402.1 Q5VXU1-1
NKAIN2ENST00000368416.5 linkc.273+6095A>G intron_variant Intron 3 of 3 1 ENSP00000357401.1 Q5VXU1-2
NKAIN2ENST00000476571.1 linkn.397+6095A>G intron_variant Intron 4 of 4 5

Frequencies

GnomAD3 genomes
AF:
0.860
AC:
130541
AN:
151862
Hom.:
56459
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.957
Gnomad AMI
AF:
0.870
Gnomad AMR
AF:
0.868
Gnomad ASJ
AF:
0.867
Gnomad EAS
AF:
0.808
Gnomad SAS
AF:
0.838
Gnomad FIN
AF:
0.830
Gnomad MID
AF:
0.831
Gnomad NFE
AF:
0.808
Gnomad OTH
AF:
0.864
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.860
AC:
130658
AN:
151980
Hom.:
56520
Cov.:
31
AF XY:
0.862
AC XY:
64013
AN XY:
74266
show subpopulations
Gnomad4 AFR
AF:
0.957
Gnomad4 AMR
AF:
0.868
Gnomad4 ASJ
AF:
0.867
Gnomad4 EAS
AF:
0.808
Gnomad4 SAS
AF:
0.839
Gnomad4 FIN
AF:
0.830
Gnomad4 NFE
AF:
0.808
Gnomad4 OTH
AF:
0.862
Alfa
AF:
0.838
Hom.:
6651
Bravo
AF:
0.869
Asia WGS
AF:
0.820
AC:
2842
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.60
DANN
Benign
0.39

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6940582; hg19: chr6-124682588; COSMIC: COSV63649805; API