rs148337159
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_030928.4(CDT1):c.758G>A(p.Arg253His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000196 in 1,613,146 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R253C) has been classified as Uncertain significance.
Frequency
Consequence
NM_030928.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDT1 | NM_030928.4 | c.758G>A | p.Arg253His | missense_variant | 5/10 | ENST00000301019.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDT1 | ENST00000301019.9 | c.758G>A | p.Arg253His | missense_variant | 5/10 | 1 | NM_030928.4 | P1 | |
CDT1 | ENST00000569140.1 | c.29G>A | p.Arg10His | missense_variant | 1/5 | 3 | |||
CDT1 | ENST00000562747.1 | n.464G>A | non_coding_transcript_exon_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000769 AC: 117AN: 152208Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.000372 AC: 93AN: 249804Hom.: 0 AF XY: 0.000317 AC XY: 43AN XY: 135546
GnomAD4 exome AF: 0.000136 AC: 199AN: 1460820Hom.: 0 Cov.: 69 AF XY: 0.000139 AC XY: 101AN XY: 726692
GnomAD4 genome AF: 0.000768 AC: 117AN: 152326Hom.: 0 Cov.: 35 AF XY: 0.000738 AC XY: 55AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 24, 2017 | - - |
CDT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 09, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at