chr1-245367244-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_018012.4(KIF26B):c.876C>T(p.Leu292=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0015 in 1,608,092 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0013 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 6 hom. )
Consequence
KIF26B
NM_018012.4 synonymous
NM_018012.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.251
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 -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 1-245367244-C-T is Benign according to our data. Variant chr1-245367244-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3050204.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.251 with no splicing effect.
BS2
?
High AC in GnomAd at 205 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF26B | NM_018012.4 | c.876C>T | p.Leu292= | synonymous_variant | 3/15 | ENST00000407071.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF26B | ENST00000407071.7 | c.876C>T | p.Leu292= | synonymous_variant | 3/15 | 1 | NM_018012.4 | A2 | |
KIF26B | ENST00000479506.1 | n.650C>T | non_coding_transcript_exon_variant | 2/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00135 AC: 205AN: 152238Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00103 AC: 244AN: 236662Hom.: 2 AF XY: 0.00112 AC XY: 143AN XY: 128224
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GnomAD4 exome AF: 0.00151 AC: 2201AN: 1455736Hom.: 6 Cov.: 32 AF XY: 0.00147 AC XY: 1066AN XY: 723464
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GnomAD4 genome ? AF: 0.00135 AC: 205AN: 152356Hom.: 1 Cov.: 32 AF XY: 0.00146 AC XY: 109AN XY: 74506
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
KIF26B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 23, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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