chr16-88808158-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_030928.4(CDT1):c.1521G>A(p.Pro507=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00146 in 1,612,770 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P507P) has been classified as Likely benign.
Frequency
Consequence
NM_030928.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDT1 | NM_030928.4 | c.1521G>A | p.Pro507= | synonymous_variant | 10/10 | ENST00000301019.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDT1 | ENST00000301019.9 | c.1521G>A | p.Pro507= | synonymous_variant | 10/10 | 1 | NM_030928.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00715 AC: 1089AN: 152222Hom.: 18 Cov.: 34
GnomAD3 exomes AF: 0.00199 AC: 493AN: 248008Hom.: 3 AF XY: 0.00150 AC XY: 203AN XY: 134932
GnomAD4 exome AF: 0.000862 AC: 1259AN: 1460430Hom.: 15 Cov.: 31 AF XY: 0.000805 AC XY: 585AN XY: 726506
GnomAD4 genome AF: 0.00719 AC: 1096AN: 152340Hom.: 19 Cov.: 34 AF XY: 0.00698 AC XY: 520AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 13, 2016 | - - |
Adenine phosphoribosyltransferase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 18, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at