chr8-144467619-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001369769.2(KIFC2):c.604A>T(p.Ile202Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00536 in 1,593,904 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001369769.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIFC2 | NM_001369769.2 | c.604A>T | p.Ile202Phe | missense_variant | 5/18 | ENST00000645548.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIFC2 | ENST00000645548.2 | c.604A>T | p.Ile202Phe | missense_variant | 5/18 | NM_001369769.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00338 AC: 515AN: 152182Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00309 AC: 724AN: 234294Hom.: 2 AF XY: 0.00318 AC XY: 403AN XY: 126582
GnomAD4 exome AF: 0.00557 AC: 8028AN: 1441604Hom.: 34 Cov.: 35 AF XY: 0.00534 AC XY: 3824AN XY: 715482
GnomAD4 genome ? AF: 0.00337 AC: 514AN: 152300Hom.: 3 Cov.: 33 AF XY: 0.00306 AC XY: 228AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | KIFC2: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at