16-88804608-A-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_030928.4(CDT1):āc.292A>Gā(p.Ile98Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000768 in 1,612,900 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I98T) has been classified as Uncertain significance.
Frequency
Consequence
NM_030928.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDT1 | NM_030928.4 | c.292A>G | p.Ile98Val | missense_variant | 2/10 | ENST00000301019.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDT1 | ENST00000301019.9 | c.292A>G | p.Ile98Val | missense_variant | 2/10 | 1 | NM_030928.4 | P1 | |
CDT1 | ENST00000562747.1 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00386 AC: 587AN: 152126Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00132 AC: 329AN: 249024Hom.: 0 AF XY: 0.000917 AC XY: 124AN XY: 135204
GnomAD4 exome AF: 0.000445 AC: 650AN: 1460656Hom.: 3 Cov.: 33 AF XY: 0.000403 AC XY: 293AN XY: 726602
GnomAD4 genome AF: 0.00387 AC: 589AN: 152244Hom.: 4 Cov.: 33 AF XY: 0.00404 AC XY: 301AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | CDT1: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 19, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at