rs9332437
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001304533.3(NKAIN3):c.472-78271C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,780 control chromosomes in the GnomAD database, including 28,450 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 0.60 ( 28450 hom., cov: 30)
Consequence
NKAIN3
NM_001304533.3 intron
NM_001304533.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0540
Genes affected
NKAIN3 (HGNC:26829): (sodium/potassium transporting ATPase interacting 3) NKAIN3 is a member of a family of mammalian proteins (see NKAIN1; MIM 612871) with similarity to Drosophila Nkain (Gorokhova et al., 2007 [PubMed 17606467]).[supplied by OMIM, Jun 2009]
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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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NKAIN3 | NM_001304533.3 | c.472-78271C>T | intron_variant | ENST00000623646.3 | |||
NKAIN3 | NM_001410914.1 | c.472-78271C>T | intron_variant | ||||
NKAIN3 | XM_017013359.2 | c.472-78271C>T | intron_variant | ||||
NKAIN3 | NR_130764.2 | n.692-78271C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NKAIN3 | ENST00000623646.3 | c.472-78271C>T | intron_variant | NM_001304533.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.604 AC: 91530AN: 151662Hom.: 28429 Cov.: 30
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.603 AC: 91586AN: 151780Hom.: 28450 Cov.: 30 AF XY: 0.596 AC XY: 44172AN XY: 74174
GnomAD4 genome
?
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44172
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74174
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1654
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3474
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