chr8-29070566-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015254.4(KIF13B):c.5419G>A(p.Ala1807Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,606,492 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1807D) has been classified as Uncertain significance.
Frequency
Consequence
NM_015254.4 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 | UniProt |
---|---|---|---|---|---|---|---|
KIF13B | NM_015254.4 | c.5419G>A | p.Ala1807Thr | missense_variant | 40/40 | ENST00000524189.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF13B | ENST00000524189.6 | c.5419G>A | p.Ala1807Thr | missense_variant | 40/40 | 1 | NM_015254.4 | P1 | |
KIF13B | ENST00000523130.1 | c.1195G>A | p.Ala399Thr | missense_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000432 AC: 10AN: 231402Hom.: 0 AF XY: 0.00000788 AC XY: 1AN XY: 126958
GnomAD4 exome AF: 0.0000138 AC: 20AN: 1454326Hom.: 0 Cov.: 32 AF XY: 0.00000692 AC XY: 5AN XY: 722862
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2021 | The c.5419G>A (p.A1807T) alteration is located in exon 40 (coding exon 40) of the KIF13B gene. This alteration results from a G to A substitution at nucleotide position 5419, causing the alanine (A) at amino acid position 1807 to be replaced by a threonine (T). 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