14-104172104-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015656.2(KIF26A):c.1326+169A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,262 control chromosomes in the GnomAD database, including 46,687 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 0.78 ( 46687 hom., cov: 36)
Consequence
KIF26A
NM_015656.2 intron
NM_015656.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.90
Genes affected
KIF26A (HGNC:20226): (kinesin family member 26A) Predicted to enable microtubule binding activity and microtubule motor activity. Predicted to be involved in enteric nervous system development; negative regulation of signal transduction; and regulation of cell growth by extracellular stimulus. Predicted to be located in cytosol. Predicted to be part of kinesin complex. Predicted to be active in microtubule. [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=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF26A | NM_015656.2 | c.1326+169A>G | intron_variant | ENST00000423312.7 | |||
KIF26A | XM_011536641.3 | c.399+169A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF26A | ENST00000423312.7 | c.1326+169A>G | intron_variant | 5 | NM_015656.2 | A2 | |||
KIF26A | ENST00000315264.7 | c.909+169A>G | intron_variant | 1 | P4 | ||||
KIF26A | ENST00000697132.1 | c.1422+169A>G | intron_variant | A2 |
Frequencies
GnomAD3 genomes AF: 0.776 AC: 118034AN: 152144Hom.: 46631 Cov.: 36
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.776 AC: 118149AN: 152262Hom.: 46687 Cov.: 36 AF XY: 0.778 AC XY: 57936AN XY: 74426
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ClinVar
Not reported inComputational scores
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Name
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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