Genetic Variant CDYL:c.1332+31delA (chr6-4943770-TA-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_004824.4(CDYL):c.1332+31delA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.10 ( 887 hom., cov: 0)

Exomes 𝑓: 0.13 ( 547 hom. )

Consequence

CDYL
NM_004824.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.378

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]

CDYL links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDYL	NM_004824.4 link	c.1332+31delA		intron_variant	Intron 5 of 6	ENST00000397588.8	NP_004815.3	Q9Y232-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDYL	ENST00000397588.8 link	c.1332+31delA		intron_variant	Intron 5 of 6	1	NM_004824.4	ENSP00000380718.3		Q9Y232-2

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

14610

AN:

144254

Hom.:

887

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0267

Gnomad AMI

AF:

0.0889

Gnomad AMR

AF:

0.0904

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.0964

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.112

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.0986

GnomAD2 exomes

AF:

0.140

AC:

19810

AN:

141918

AF XY:

0.139

show subpopulations

Gnomad AFR exome

AF:

0.144

Gnomad AMR exome

AF:

0.128

Gnomad ASJ exome

AF:

0.116

Gnomad EAS exome

AF:

0.134

Gnomad FIN exome

AF:

0.174

Gnomad NFE exome

AF:

0.135

Gnomad OTH exome

AF:

0.135

GnomAD4 exome

AF:

0.129

AC:

131301

AN:

1015622

Hom.:

547

Cov.:

AF XY:

0.130

AC XY:

65994

AN XY:

508390

show subpopulations

African (AFR)

AF:

0.0812

AC:

1963

AN:

24178

American (AMR)

AF:

0.107

AC:

2741

AN:

25596

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

1967

AN:

18352

East Asian (EAS)

AF:

0.105

AC:

3566

AN:

33860

South Asian (SAS)

AF:

0.147

AC:

8709

AN:

59206

European-Finnish (FIN)

AF:

0.171

AC:

6946

AN:

40736

Middle Eastern (MID)

AF:

0.110

AC:

321

AN:

2920

European-Non Finnish (NFE)

AF:

0.130

AC:

99699

AN:

767302

Other (OTH)

AF:

0.124

AC:

5389

AN:

43472

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.412

Heterozygous variant carriers

4458

8916

13373

17831

22289

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3746

7492

11238

14984

18730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.101

AC:

14611

AN:

144286

Hom.:

887

Cov.:

AF XY:

0.104

AC XY:

7261

AN XY:

69710

show subpopulations

African (AFR)

AF:

0.0268

AC:

1049

AN:

39074

American (AMR)

AF:

0.0904

AC:

1318

AN:

14584

Ashkenazi Jewish (ASJ)

AF:

0.103

AC:

351

AN:

3422

East Asian (EAS)

AF:

0.0961

AC:

474

AN:

4930

South Asian (SAS)

AF:

0.162

AC:

734

AN:

4518

European-Finnish (FIN)

AF:

0.195

AC:

1601

AN:

8222

Middle Eastern (MID)

AF:

0.114

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.132

AC:

8777

AN:

66368

Other (OTH)

AF:

0.0981

AC:

195

AN:

1988

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

606

1211

1817

2422

3028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.38

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

6-4943770-TAAAAAAAA-TAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over