8-29070565-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015254.4(KIF13B):c.5420C>A(p.Ala1807Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,606,510 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. A1807T) 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.5420C>A | p.Ala1807Asp | missense_variant | 40/40 | ENST00000524189.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF13B | ENST00000524189.6 | c.5420C>A | p.Ala1807Asp | missense_variant | 40/40 | 1 | NM_015254.4 | P1 | |
KIF13B | ENST00000523130.1 | c.1196C>A | p.Ala399Asp | missense_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000475 AC: 11AN: 231468Hom.: 0 AF XY: 0.00000787 AC XY: 1AN XY: 127044
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1454310Hom.: 0 Cov.: 32 AF XY: 0.00000415 AC XY: 3AN XY: 722888
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2021 | The c.5420C>A (p.A1807D) alteration is located in exon 40 (coding exon 40) of the KIF13B gene. This alteration results from a C to A substitution at nucleotide position 5420, causing the alanine (A) at amino acid position 1807 to be replaced by an aspartic acid (D). 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