chr1-245366902-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.534C>T(p.Asn178=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000411 in 1,614,050 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 0.00033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00042 ( 7 hom. )
Consequence
KIF26B
NM_018012.4 synonymous
NM_018012.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.143
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 1-245366902-C-T is Benign according to our data. Variant chr1-245366902-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3034809.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.143 with no splicing effect.
BS2
?
High AC in GnomAd at 51 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF26B | NM_018012.4 | c.534C>T | p.Asn178= | synonymous_variant | 3/15 | ENST00000407071.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF26B | ENST00000407071.7 | c.534C>T | p.Asn178= | synonymous_variant | 3/15 | 1 | NM_018012.4 | A2 | |
KIF26B | ENST00000479506.1 | n.308C>T | non_coding_transcript_exon_variant | 2/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000335 AC: 51AN: 152238Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000690 AC: 172AN: 249166Hom.: 0 AF XY: 0.000917 AC XY: 124AN XY: 135176
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GnomAD4 exome AF: 0.000419 AC: 613AN: 1461694Hom.: 7 Cov.: 32 AF XY: 0.000573 AC XY: 417AN XY: 727122
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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 | Jan 02, 2020 | 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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BayesDel_noAF
Benign
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at