chr8-144467053-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001369769.2(KIFC2):c.273C>T(p.Phe91Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000596 in 1,594,570 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 Likely benign (★).
Frequency
Consequence
NM_001369769.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIFC2 | NM_001369769.2 | c.273C>T | p.Phe91Phe | synonymous_variant | Exon 3 of 18 | ENST00000645548.2 | NP_001356698.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIFC2 | ENST00000645548.2 | c.273C>T | p.Phe91Phe | synonymous_variant | Exon 3 of 18 | NM_001369769.2 | ENSP00000494595.1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152258Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000974 AC: 21AN: 215572Hom.: 0 AF XY: 0.0000672 AC XY: 8AN XY: 119022
GnomAD4 exome AF: 0.0000569 AC: 82AN: 1442194Hom.: 0 Cov.: 65 AF XY: 0.0000517 AC XY: 37AN XY: 716034
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152376Hom.: 0 Cov.: 35 AF XY: 0.000121 AC XY: 9AN XY: 74512
ClinVar
Submissions by phenotype
not specified Benign:1
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