chr6-21201134-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017774.3(CDKAL1):āc.1408T>Cā(p.Phe470Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_017774.3 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 |
---|---|---|---|---|---|---|---|
CDKAL1 | NM_017774.3 | c.1408T>C | p.Phe470Leu | missense_variant | 15/16 | ENST00000274695.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKAL1 | ENST00000274695.8 | c.1408T>C | p.Phe470Leu | missense_variant | 15/16 | 1 | NM_017774.3 | P1 | |
CDKAL1 | ENST00000378610.1 | c.1408T>C | p.Phe470Leu | missense_variant | 13/14 | 2 | P1 | ||
CDKAL1 | ENST00000476517.1 | n.106T>C | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461026Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726740
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 19, 2024 | The c.1408T>C (p.F470L) alteration is located in exon 15 (coding exon 13) of the CDKAL1 gene. This alteration results from a T to C substitution at nucleotide position 1408, causing the phenylalanine (F) at amino acid position 470 to be replaced by a leucine (L). 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
Publications
No publications associated with this variant yet.