chr7-151054447-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000485972.6(CDK5):c.669C>T(p.Thr223=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,020 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T223T) has been classified as Likely benign.
Frequency
Consequence
ENST00000485972.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDK5 | NM_004935.4 | c.669C>T | p.Thr223= | synonymous_variant | 10/12 | ENST00000485972.6 | NP_004926.1 | |
CDK5 | NM_001164410.3 | c.573C>T | p.Thr191= | synonymous_variant | 9/11 | NP_001157882.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDK5 | ENST00000485972.6 | c.669C>T | p.Thr223= | synonymous_variant | 10/12 | 1 | NM_004935.4 | ENSP00000419782 | P1 | |
CDK5 | ENST00000297518.4 | c.573C>T | p.Thr191= | synonymous_variant | 9/11 | 1 | ENSP00000297518 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152032Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248394Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134678
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1460988Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 726752
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152032Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74264
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at