chr6-21201136-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017774.3(CDKAL1):c.1410C>A(p.Phe470Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,613,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.1410C>A | p.Phe470Leu | missense_variant | 15/16 | ENST00000274695.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKAL1 | ENST00000274695.8 | c.1410C>A | p.Phe470Leu | missense_variant | 15/16 | 1 | NM_017774.3 | P1 | |
CDKAL1 | ENST00000378610.1 | c.1410C>A | p.Phe470Leu | missense_variant | 13/14 | 2 | P1 | ||
CDKAL1 | ENST00000476517.1 | n.108C>A | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251370Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135850
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1460932Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 726710
GnomAD4 genome ? AF: 0.0000986 AC: 15AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 23, 2021 | The c.1410C>A (p.F470L) alteration is located in exon 15 (coding exon 13) of the CDKAL1 gene. This alteration results from a C to A substitution at nucleotide position 1410, 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