chr6-124202310-C-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001040214.3(NKAIN2):c.55-80695C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 151,982 control chromosomes in the GnomAD database, including 489 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 0.058 ( 489 hom., cov: 32)
Consequence
NKAIN2
NM_001040214.3 intron
NM_001040214.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.197
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NKAIN2 | ENST00000368417.6 | c.55-80695C>A | intron_variant | Intron 1 of 6 | 5 | NM_001040214.3 | ENSP00000357402.1 | |||
NKAIN2 | ENST00000368416.5 | c.55-80695C>A | intron_variant | Intron 1 of 3 | 1 | ENSP00000357401.1 | ||||
NKAIN2 | ENST00000476571.1 | n.178+80369C>A | intron_variant | Intron 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0577 AC: 8767AN: 151864Hom.: 484 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
8767
AN:
151864
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0578 AC: 8787AN: 151982Hom.: 489 Cov.: 32 AF XY: 0.0605 AC XY: 4492AN XY: 74288 show subpopulations
GnomAD4 genome
AF:
AC:
8787
AN:
151982
Hom.:
Cov.:
32
AF XY:
AC XY:
4492
AN XY:
74288
show subpopulations
African (AFR)
AF:
AC:
5173
AN:
41488
American (AMR)
AF:
AC:
1526
AN:
15216
Ashkenazi Jewish (ASJ)
AF:
AC:
144
AN:
3464
East Asian (EAS)
AF:
AC:
379
AN:
5168
South Asian (SAS)
AF:
AC:
217
AN:
4824
European-Finnish (FIN)
AF:
AC:
190
AN:
10606
Middle Eastern (MID)
AF:
AC:
7
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1054
AN:
67900
Other (OTH)
AF:
AC:
96
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
395
791
1186
1582
1977
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
92
184
276
368
460
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
199
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.