chr8-144466443-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001369769.2(KIFC2):c.24C>T(p.Leu8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,363,372 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0028 ( 1 hom., cov: 30)
Exomes 𝑓: 0.0016 ( 29 hom. )
Consequence
KIFC2
NM_001369769.2 synonymous
NM_001369769.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0820
Genes affected
KIFC2 (HGNC:29530): (kinesin family member C2) Predicted to enable microtubule binding activity and microtubule motor activity. Predicted to be involved in microtubule-based movement and mitotic spindle assembly. Predicted to be located in cytoplasm. Predicted to be part of kinesin complex. Predicted to be active in microtubule cytoskeleton and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 8-144466443-C-T is Benign according to our data. Variant chr8-144466443-C-T is described in ClinVar as [Benign]. Clinvar id is 782144.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.082 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00278 (417/150082) while in subpopulation SAS AF= 0.0193 (93/4814). AF 95% confidence interval is 0.0161. There are 1 homozygotes in gnomad4. There are 223 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome at 7 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIFC2 | NM_001369769.2 | c.24C>T | p.Leu8= | synonymous_variant | 1/18 | ENST00000645548.2 | |
TMEM276 | NM_001408062.1 | c.-196+510G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIFC2 | ENST00000645548.2 | c.24C>T | p.Leu8= | synonymous_variant | 1/18 | NM_001369769.2 | P1 | ||
KIFC2 | ENST00000301332.3 | c.24C>T | p.Leu8= | synonymous_variant | 1/17 | 1 | |||
KIFC2 | ENST00000642354.1 | c.24C>T | p.Leu8= | synonymous_variant | 1/18 | ||||
KIFC2 | ENST00000643461.1 | n.401C>T | non_coding_transcript_exon_variant | 1/17 |
Frequencies
GnomAD3 genomes ? AF: 0.00272 AC: 408AN: 149974Hom.: 1 Cov.: 30
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GnomAD3 exomes AF: 0.00350 AC: 488AN: 139430Hom.: 7 AF XY: 0.00434 AC XY: 349AN XY: 80352
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GnomAD4 exome AF: 0.00159 AC: 1933AN: 1213290Hom.: 29 Cov.: 29 AF XY: 0.00190 AC XY: 1140AN XY: 600682
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GnomAD4 genome ? AF: 0.00278 AC: 417AN: 150082Hom.: 1 Cov.: 30 AF XY: 0.00304 AC XY: 223AN XY: 73310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 28, 2017 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at