6-17764207-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022113.6(KIF13A):c.5321C>T(p.Ser1774Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022113.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF13A | NM_022113.6 | c.5321C>T | p.Ser1774Phe | missense_variant | 39/39 | ENST00000259711.11 | NP_071396.4 | |
KIF13A | NM_001105566.3 | c.5216C>T | p.Ser1739Phe | missense_variant | 38/38 | NP_001099036.1 | ||
KIF13A | NM_001105567.3 | c.5177C>T | p.Ser1726Phe | missense_variant | 37/37 | NP_001099037.1 | ||
KIF13A | NM_001105568.4 | c.5177C>T | p.Ser1726Phe | missense_variant | 37/38 | NP_001099038.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF13A | ENST00000259711.11 | c.5321C>T | p.Ser1774Phe | missense_variant | 39/39 | 1 | NM_022113.6 | ENSP00000259711.6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461710Hom.: 0 Cov.: 34 AF XY: 0.00000825 AC XY: 6AN XY: 727138
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | The c.5321C>T (p.S1774F) alteration is located in exon 39 (coding exon 39) of the KIF13A gene. This alteration results from a C to T substitution at nucleotide position 5321, causing the serine (S) at amino acid position 1774 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.