chr18-48758133-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_014772.3(CTIF):c.799G>A(p.Ala267Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000973 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014772.3 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 |
---|---|---|---|---|---|---|---|
CTIF | NM_014772.3 | c.799G>A | p.Ala267Thr | missense_variant | 8/12 | ENST00000256413.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTIF | ENST00000256413.8 | c.799G>A | p.Ala267Thr | missense_variant | 8/12 | 1 | NM_014772.3 | A1 | |
CTIF | ENST00000382998.8 | c.799G>A | p.Ala267Thr | missense_variant | 9/13 | 1 | P3 | ||
CTIF | ENST00000587769.1 | n.451G>A | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000199 AC: 50AN: 250934Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135690
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461826Hom.: 0 Cov.: 32 AF XY: 0.000131 AC XY: 95AN XY: 727212
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74404
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2021 | 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