chrX-70330248-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_012310.5(KIF4A):c.987T>C(p.Tyr329=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 1,209,552 control chromosomes in the GnomAD database, including 1,572 homozygotes. There are 23,917 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.056 ( 154 hom., 1887 hem., cov: 22)
Exomes 𝑓: 0.056 ( 1418 hom. 22030 hem. )
Consequence
KIF4A
NM_012310.5 synonymous
NM_012310.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.416
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 Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant X-70330248-T-C is Benign according to our data. Variant chrX-70330248-T-C is described in ClinVar as [Benign]. Clinvar id is 1300075.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-70330248-T-C is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=0.416 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF4A | NM_012310.5 | c.987T>C | p.Tyr329= | synonymous_variant | 9/31 | ENST00000374403.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF4A | ENST00000374403.4 | c.987T>C | p.Tyr329= | synonymous_variant | 9/31 | 1 | NM_012310.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0561 AC: 6275AN: 111784Hom.: 153 Cov.: 22 AF XY: 0.0553 AC XY: 1879AN XY: 33962
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GnomAD3 exomes AF: 0.0776 AC: 14205AN: 183017Hom.: 457 AF XY: 0.0804 AC XY: 5433AN XY: 67611
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GnomAD4 exome AF: 0.0565 AC: 62017AN: 1097712Hom.: 1418 Cov.: 30 AF XY: 0.0607 AC XY: 22030AN XY: 363182
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GnomAD4 genome ? AF: 0.0562 AC: 6281AN: 111840Hom.: 154 Cov.: 22 AF XY: 0.0555 AC XY: 1887AN XY: 34028
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual disability, X-linked 100 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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