rs34649909
Positions:
- chr6-4943770-TAAAAAAAA-T
- chr6-4943770-TAAAAAAAA-TAAAA
- chr6-4943770-TAAAAAAAA-TAAAAA
- chr6-4943770-TAAAAAAAA-TAAAAAA
- chr6-4943770-TAAAAAAAA-TAAAAAAA
- chr6-4943770-TAAAAAAAA-TAAAAAAAAA
- chr6-4943770-TAAAAAAAA-TAAAAAAAAAA
- chr6-4943770-TAAAAAAAA-TAAAAAAAAAAA
- chr6-4943770-TAAAAAAAA-TAAAAAAAAAAAA
- chr6-4943770-TAAAAAAAA-TAAAAAAAAAAAAA
- chr6-4943770-TAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004824.4(CDYL):c.1332+24_1332+31del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000972 in 1,029,136 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 9.7e-7 ( 0 hom. )
Consequence
CDYL
NM_004824.4 intron
NM_004824.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.433
Genes affected
CDYL (HGNC:1811): (chromodomain Y like) Chromodomain Y is a primate-specific Y-chromosomal gene family expressed exclusively in the testis and implicated in infertility. Although the Y-linked genes are testis-specific, this autosomal gene is ubiquitously expressed. The Y-linked genes arose by retrotransposition of an mRNA from this gene, followed by amplification of the retroposed gene. Proteins encoded by this gene superfamily possess a chromodomain, a motif implicated in chromatin binding and gene suppression, and a catalytic domain believed to be involved in histone acetylation. Multiple proteins are encoded by transcript variants of this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDYL | NM_004824.4 | c.1332+24_1332+31del | intron_variant | ENST00000397588.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDYL | ENST00000397588.8 | c.1332+24_1332+31del | intron_variant | 1 | NM_004824.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 0
GnomAD3 genomes
?
Cov.:
0
GnomAD4 exome AF: 9.72e-7 AC: 1AN: 1029136Hom.: 0 AF XY: 0.00000194 AC XY: 1AN XY: 515290
GnomAD4 exome
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1
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1029136
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1
AN XY:
515290
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GnomAD4 genome ? Cov.: 0
GnomAD4 genome
?
Cov.:
0
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at