rs13204086
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001040214.3(NKAIN2):c.55-198995C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 151,972 control chromosomes in the GnomAD database, including 49 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 0.018 ( 49 hom., cov: 32)
Consequence
NKAIN2
NM_001040214.3 intron
NM_001040214.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.663
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=-1.02).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0182 (2761/151972) while in subpopulation NFE AF= 0.0264 (1790/67916). AF 95% confidence interval is 0.0253. There are 49 homozygotes in gnomad4. There are 1306 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 49 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKAIN2 | NM_001040214.3 | c.55-198995C>T | intron_variant | ENST00000368417.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKAIN2 | ENST00000368417.6 | c.55-198995C>T | intron_variant | 5 | NM_001040214.3 | P1 | |||
NKAIN2 | ENST00000368416.5 | c.55-198995C>T | intron_variant | 1 | |||||
NKAIN2 | ENST00000476571.1 | n.115-37868C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0182 AC: 2762AN: 151854Hom.: 49 Cov.: 32
GnomAD3 genomes
?
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2762
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151854
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0182 AC: 2761AN: 151972Hom.: 49 Cov.: 32 AF XY: 0.0176 AC XY: 1306AN XY: 74266
GnomAD4 genome
?
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2761
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32
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1306
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74266
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at