chr1-245367144-G-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018012.4(KIF26B):c.776G>T(p.Gly259Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000745 in 1,601,854 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00050 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00077 ( 13 hom. )
Consequence
KIF26B
NM_018012.4 missense
NM_018012.4 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 2.52
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 Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0055597723).
BP6
Variant 1-245367144-G-T is Benign according to our data. Variant chr1-245367144-G-T is described in ClinVar as [Benign]. Clinvar id is 3048017.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 76 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF26B | NM_018012.4 | c.776G>T | p.Gly259Val | missense_variant | 3/15 | ENST00000407071.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF26B | ENST00000407071.7 | c.776G>T | p.Gly259Val | missense_variant | 3/15 | 1 | NM_018012.4 | A2 | |
KIF26B | ENST00000479506.1 | n.550G>T | non_coding_transcript_exon_variant | 2/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000499 AC: 76AN: 152234Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00160 AC: 363AN: 226496Hom.: 5 AF XY: 0.00211 AC XY: 259AN XY: 122522
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GnomAD4 exome AF: 0.000771 AC: 1117AN: 1449502Hom.: 13 Cov.: 32 AF XY: 0.00111 AC XY: 799AN XY: 719760
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GnomAD4 genome AF: 0.000499 AC: 76AN: 152352Hom.: 2 Cov.: 32 AF XY: 0.000711 AC XY: 53AN XY: 74510
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
KIF26B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 06, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
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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