chr16-80604501-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_152342.4(CDYL2):c.1408G>T(p.Val470Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,890 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 Uncertain significance (★).
Frequency
Consequence
NM_152342.4 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDYL2 | NM_152342.4 | c.1408G>T | p.Val470Leu | missense_variant | Exon 7 of 7 | ENST00000570137.7 | NP_689555.2 | |
CDYL2 | XM_011522866.2 | c.1510G>T | p.Val504Leu | missense_variant | Exon 7 of 7 | XP_011521168.1 | ||
CDYL2 | XM_011522867.3 | c.1399G>T | p.Val467Leu | missense_variant | Exon 7 of 7 | XP_011521169.1 | ||
CDYL2 | XM_024450151.2 | c.1231G>T | p.Val411Leu | missense_variant | Exon 7 of 7 | XP_024305919.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDYL2 | ENST00000570137.7 | c.1408G>T | p.Val470Leu | missense_variant | Exon 7 of 7 | 1 | NM_152342.4 | ENSP00000476295.1 | ||
CDYL2 | ENST00000562812.5 | c.1411G>T | p.Val471Leu | missense_variant | Exon 8 of 8 | 5 | ENSP00000454546.1 | |||
CDYL2 | ENST00000563890.5 | c.1411G>T | p.Val471Leu | missense_variant | Exon 8 of 8 | 5 | ENSP00000455111.1 | |||
CDYL2 | ENST00000566173.3 | c.1411G>T | p.Val471Leu | missense_variant | Exon 8 of 8 | 5 | ENSP00000456934.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727246
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1408G>T (p.V470L) alteration is located in exon 7 (coding exon 7) of the CDYL2 gene. This alteration results from a G to T substitution at nucleotide position 1408, causing the valine (V) 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