chr6-33404095-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_002263.4(KIFC1):c.722G>A(p.Arg241Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,732 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 Uncertain significance (★).
Frequency
Consequence
NM_002263.4 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 |
---|---|---|---|---|---|---|---|
KIFC1 | NM_002263.4 | c.722G>A | p.Arg241Gln | missense_variant | 6/11 | ENST00000428849.7 | |
KIFC1 | XM_011514585.2 | c.722G>A | p.Arg241Gln | missense_variant | 6/12 | ||
KIFC1 | XM_017010837.2 | c.599G>A | p.Arg200Gln | missense_variant | 6/11 | ||
KIFC1 | XM_011514587.3 | c.722G>A | p.Arg241Gln | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIFC1 | ENST00000428849.7 | c.722G>A | p.Arg241Gln | missense_variant | 6/11 | 1 | NM_002263.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250784Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135506
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461524Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727058
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.722G>A (p.R241Q) alteration is located in exon 6 (coding exon 6) of the KIFC1 gene. This alteration results from a G to A substitution at nucleotide position 722, causing the arginine (R) at amino acid position 241 to be replaced by a glutamine (Q). 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