6-4892077-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_004824.4(CDYL):c.389G>A(p.Arg130Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,614,096 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R130W) has been classified as Uncertain significance.
Frequency
Consequence
NM_004824.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDYL | NM_004824.4 | c.389G>A | p.Arg130Gln | missense_variant | 2/7 | ENST00000397588.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDYL | ENST00000397588.8 | c.389G>A | p.Arg130Gln | missense_variant | 2/7 | 1 | NM_004824.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152208Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251460Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135892
GnomAD4 exome AF: 0.000107 AC: 157AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.000120 AC XY: 87AN XY: 727244
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152208Hom.: 1 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2024 | The c.389G>A (p.R130Q) alteration is located in exon 2 (coding exon 2) of the CDYL gene. This alteration results from a G to A substitution at nucleotide position 389, causing the arginine (R) at amino acid position 130 to be replaced by a glutamine (Q). 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