rs10496694
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_207363.3(NCKAP5):c.5049+2458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0597 in 152,212 control chromosomes in the GnomAD database, including 360 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 0.060 ( 360 hom., cov: 33)
Consequence
NCKAP5
NM_207363.3 intron
NM_207363.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.532
Genes affected
NCKAP5 (HGNC:29847): (NCK associated protein 5) Predicted to be involved in microtubule bundle formation and microtubule depolymerization. Predicted to be active in microtubule plus-end. [provided by Alliance of Genome Resources, Apr 2022]
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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=-1.0).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0845 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCKAP5 | NM_207363.3 | c.5049+2458C>T | intron_variant | ENST00000409261.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCKAP5 | ENST00000409261.6 | c.5049+2458C>T | intron_variant | 5 | NM_207363.3 | P1 | |||
ENST00000651100.1 | n.458-36007G>A | intron_variant, non_coding_transcript_variant | |||||||
NCKAP5 | ENST00000409213.5 | c.1093-4700C>T | intron_variant | 5 | |||||
NCKAP5 | ENST00000473859.1 | n.262+2458C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0598 AC: 9090AN: 152094Hom.: 360 Cov.: 33
GnomAD3 genomes
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9090
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152094
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0597 AC: 9085AN: 152212Hom.: 360 Cov.: 33 AF XY: 0.0597 AC XY: 4446AN XY: 74418
GnomAD4 genome
?
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AC:
9085
AN:
152212
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33
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4446
AN XY:
74418
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110
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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