chr8-29072037-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015254.4(KIF13B):c.4801G>A(p.Ala1601Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000924 in 1,299,372 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_015254.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF13B | NM_015254.4 | c.4801G>A | p.Ala1601Thr | missense_variant | 39/40 | ENST00000524189.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF13B | ENST00000524189.6 | c.4801G>A | p.Ala1601Thr | missense_variant | 39/40 | 1 | NM_015254.4 | P1 | |
KIF13B | ENST00000523130.1 | c.577G>A | p.Ala193Thr | missense_variant | 4/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151692Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000784 AC: 9AN: 1147572Hom.: 0 Cov.: 32 AF XY: 0.00000365 AC XY: 2AN XY: 548188
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151800Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74240
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 13, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at