chr16-4513004-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013399.3(CDIP1):c.302C>T(p.Thr101Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000314 in 1,590,014 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T101K) has been classified 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.302C>T | p.Thr101Met | missense_variant | 5/6 | ENST00000567695.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDIP1 | ENST00000567695.6 | c.302C>T | p.Thr101Met | missense_variant | 5/6 | 1 | NM_013399.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000147 AC: 3AN: 203502Hom.: 0 AF XY: 0.0000181 AC XY: 2AN XY: 110660
GnomAD4 exome AF: 0.0000320 AC: 46AN: 1437916Hom.: 0 Cov.: 34 AF XY: 0.0000266 AC XY: 19AN XY: 713132
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2024 | The c.302C>T (p.T101M) alteration is located in exon 5 (coding exon 3) of the CDIP1 gene. This alteration results from a C to T substitution at nucleotide position 302, causing the threonine (T) at amino acid position 101 to be replaced by a methionine (M). 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