X-70297015-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_012310.5(KIF4A):c.253C>T(p.Leu85=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000082 in 1,097,618 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 23)
Exomes 𝑓: 0.0000082 ( 0 hom. 3 hem. )
Consequence
KIF4A
NM_012310.5 synonymous
NM_012310.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.791
Genes affected
KIF4A (HGNC:13339): (kinesin family member 4A) This gene encodes a member of the kinesin 4 subfamily of kinesin related proteins. The encoded protein is an ATP dependent microtubule-based motor protein that is involved in the intracellular transport of membranous organelles. This protein also associates with condensed chromosome arms and may be involved in maintaining chromosome integrity during mitosis. This protein may also be involved in the organization of the central spindle prior to cytokinesis. A pseudogene of this gene is found on chromosome X.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
?
Variant X-70297015-C-T is Benign according to our data. Variant chrX-70297015-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 753279.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.791 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF4A | NM_012310.5 | c.253C>T | p.Leu85= | synonymous_variant | 4/31 | ENST00000374403.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF4A | ENST00000374403.4 | c.253C>T | p.Leu85= | synonymous_variant | 4/31 | 1 | NM_012310.5 | P1 | |
KIF4A | ENST00000485406.1 | n.498C>T | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 182087Hom.: 0 AF XY: 0.0000150 AC XY: 1AN XY: 66587
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GnomAD4 exome AF: 0.00000820 AC: 9AN: 1097618Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 3AN XY: 363016
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GnomAD4 genome ? Cov.: 23
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 15, 2018 | - - |
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