chr10-32015608-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004521.3(KIF5B):c.2813G>A(p.Ser938Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,678 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_004521.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF5B | NM_004521.3 | c.2813G>A | p.Ser938Asn | missense_variant | Exon 25 of 26 | ENST00000302418.5 | NP_004512.1 | |
KIF5B | XM_047425202.1 | c.2813G>A | p.Ser938Asn | missense_variant | Exon 25 of 25 | XP_047281158.1 | ||
KIF5B | XM_047425203.1 | c.2531G>A | p.Ser844Asn | missense_variant | Exon 26 of 27 | XP_047281159.1 | ||
LOC107984219 | XR_001747415.2 | n.5354-2418C>T | intron_variant | Intron 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251310Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135836
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1461480Hom.: 0 Cov.: 30 AF XY: 0.0000426 AC XY: 31AN XY: 727094
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2813G>A (p.S938N) alteration is located in exon 25 (coding exon 25) of the KIF5B gene. This alteration results from a G to A substitution at nucleotide position 2813, causing the serine (S) at amino acid position 938 to be replaced by an asparagine (N). 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