chr8-144466500-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001369769.2(KIFC2):c.81G>C(p.Glu27Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000229 in 1,307,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIFC2 | NM_001369769.2 | c.81G>C | p.Glu27Asp | missense_variant | 1/18 | ENST00000645548.2 | |
TMEM276 | NM_001408062.1 | c.-196+453C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIFC2 | ENST00000645548.2 | c.81G>C | p.Glu27Asp | missense_variant | 1/18 | NM_001369769.2 | P1 | ||
KIFC2 | ENST00000301332.3 | c.81G>C | p.Glu27Asp | missense_variant | 1/17 | 1 | |||
KIFC2 | ENST00000642354.1 | c.81G>C | p.Glu27Asp | missense_variant | 1/18 | ||||
KIFC2 | ENST00000643461.1 | n.458G>C | non_coding_transcript_exon_variant | 1/17 |
Frequencies
GnomAD3 genomes ? AF: 0.00000666 AC: 1AN: 150110Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000173 AC: 2AN: 1157480Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 567674
GnomAD4 genome ? AF: 0.00000666 AC: 1AN: 150110Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73244
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | 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