chr1-245366988-A-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_018012.4(KIF26B):āc.620A>Cā(p.Gln207Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000821 in 1,461,596 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000082 ( 0 hom. )
Consequence
KIF26B
NM_018012.4 missense
NM_018012.4 missense
Scores
1
10
8
Clinical Significance
Conservation
PhyloP100: 4.71
Genes affected
KIF26B (HGNC:25484): (kinesin family member 26B) The protein encoded by this gene is an intracellular motor protein thought to transport organelles along microtubules. The encoded protein is required for kidney development. Elevated levels of this protein have been found in some breast and colorectal cancers. [provided by RefSeq, Mar 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF26B | NM_018012.4 | c.620A>C | p.Gln207Pro | missense_variant | 3/15 | ENST00000407071.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF26B | ENST00000407071.7 | c.620A>C | p.Gln207Pro | missense_variant | 3/15 | 1 | NM_018012.4 | A2 | |
KIF26B | ENST00000479506.1 | n.394A>C | non_coding_transcript_exon_variant | 2/4 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 248842Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135076
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GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461596Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727090
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GnomAD4 genome Cov.: 32
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32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.620A>C (p.Q207P) alteration is located in exon 3 (coding exon 3) of the KIF26B gene. This alteration results from a A to C substitution at nucleotide position 620, causing the glutamine (Q) at amino acid position 207 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Gain of glycosylation at S211 (P = 0.0719);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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