chr8-29071946-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015254.4(KIF13B):āc.4892G>Cā(p.Gly1631Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000225 in 1,376,328 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015254.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF13B | NM_015254.4 | c.4892G>C | p.Gly1631Ala | missense_variant | 39/40 | ENST00000524189.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF13B | ENST00000524189.6 | c.4892G>C | p.Gly1631Ala | missense_variant | 39/40 | 1 | NM_015254.4 | P1 | |
KIF13B | ENST00000523130.1 | c.668G>C | p.Gly223Ala | missense_variant | 4/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151454Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000229 AC: 28AN: 1224874Hom.: 0 Cov.: 32 AF XY: 0.0000150 AC XY: 9AN XY: 598024
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151454Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73978
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2022 | The c.4892G>C (p.G1631A) alteration is located in exon 39 (coding exon 39) of the KIF13B gene. This alteration results from a G to C substitution at nucleotide position 4892, causing the glycine (G) at amino acid position 1631 to be replaced by an alanine (A). 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