16-4514091-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013399.3(CDIP1):c.40A>G(p.Thr14Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000288 in 1,389,814 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_013399.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDIP1 | NM_013399.3 | c.40A>G | p.Thr14Ala | missense_variant | 3/6 | ENST00000567695.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDIP1 | ENST00000567695.6 | c.40A>G | p.Thr14Ala | missense_variant | 3/6 | 1 | NM_013399.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000113 AC: 2AN: 177332Hom.: 0 AF XY: 0.0000201 AC XY: 2AN XY: 99604
GnomAD4 exome AF: 0.00000288 AC: 4AN: 1389814Hom.: 0 Cov.: 30 AF XY: 0.00000579 AC XY: 4AN XY: 690498
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.40A>G (p.T14A) alteration is located in exon 3 (coding exon 1) of the CDIP1 gene. This alteration results from a A to G substitution at nucleotide position 40, causing the threonine (T) at amino acid position 14 to be replaced by an alanine (A). 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