GeneBe

rs34649909

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_004824.4(CDYL):​c.1332+24_1332+31delAAAAAAAA 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.433

Publications

0 publications found
Variant links:
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 was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004824.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CDYL
NM_004824.4
MANE Select
c.1332+24_1332+31delAAAAAAAA
intron
N/ANP_004815.3
CDYL
NM_001368125.1
c.1494+24_1494+31delAAAAAAAA
intron
N/ANP_001355054.1Q9Y232-1
CDYL
NM_001368126.1
c.1266+24_1266+31delAAAAAAAA
intron
N/ANP_001355055.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CDYL
ENST00000397588.8
TSL:1 MANE Select
c.1332+24_1332+31delAAAAAAAA
intron
N/AENSP00000380718.3Q9Y232-2
CDYL
ENST00000328908.9
TSL:1
c.1494+24_1494+31delAAAAAAAA
intron
N/AENSP00000330512.5Q9Y232-1
CDYL
ENST00000343762.5
TSL:1
c.936+24_936+31delAAAAAAAA
intron
N/AENSP00000340908.5Q9Y232-4

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
9.72e-7
AC:
1
AN:
1029136
Hom.:
0
AF XY:
0.00000194
AC XY:
1
AN XY:
515290
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
24622
American (AMR)
AF:
0.00
AC:
0
AN:
25994
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
18564
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34504
South Asian (SAS)
AF:
0.00
AC:
0
AN:
60032
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
41260
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2960
European-Non Finnish (NFE)
AF:
0.00000129
AC:
1
AN:
777124
Other (OTH)
AF:
0.00
AC:
0
AN:
44076
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs34649909; hg19: chr6-4944004; API