Genetic Variant CDYL:c.1332+30_1332+31dupAA (chr6-4943770-T-TAA) – 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+30_1332+31dupAA 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 0.092 ( 665 hom., cov: 0)

Exomes 𝑓: 0.12 ( 210 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 (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDYL	NM_004824.4 link	c.1332+30_1332+31dupAA		intron_variant	Intron 5 of 6	ENST00000397588.8	NP_004815.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDYL	ENST00000397588.8 link	c.1332+30_1332+31dupAA		intron_variant	Intron 5 of 6	1	NM_004824.4	ENSP00000380718.3

Frequencies

GnomAD3 genomes

AF:

0.0925

AC:

13340

AN:

144264

Hom.:

668

Cov.:

show subpopulations

Gnomad AFR

AF:

0.119

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.0583

Gnomad ASJ

AF:

0.0964

Gnomad EAS

AF:

0.0689

Gnomad SAS

AF:

0.0555

Gnomad FIN

AF:

0.0972

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0855

Gnomad OTH

AF:

0.0863

GnomAD2 exomes

AF:

0.0842

AC:

11951

AN:

141918

AF XY:

0.0820

show subpopulations

Gnomad AFR exome

AF:

0.104

Gnomad AMR exome

AF:

0.0537

Gnomad ASJ exome

AF:

0.0975

Gnomad EAS exome

AF:

0.0706

Gnomad FIN exome

AF:

0.103

Gnomad NFE exome

AF:

0.0895

Gnomad OTH exome

AF:

0.0961

GnomAD4 exome

AF:

0.121

AC:

122684

AN:

1016214

Hom.:

210

Cov.:

AF XY:

0.119

AC XY:

60438

AN XY:

508788

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.110

AC:

2673

AN:

24202

American (AMR)

AF:

0.0635

AC:

1630

AN:

25650

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

2168

AN:

18222

East Asian (EAS)

AF:

0.0841

AC:

2852

AN:

33908

South Asian (SAS)

AF:

0.0913

AC:

5413

AN:

59320

European-Finnish (FIN)

AF:

0.112

AC:

4530

AN:

40550

Middle Eastern (MID)

AF:

0.111

AC:

325

AN:

2932

European-Non Finnish (NFE)

AF:

0.128

AC:

98010

AN:

767950

Other (OTH)

AF:

0.117

AC:

5083

AN:

43480

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.362

Heterozygous variant carriers

6454

12908

19363

25817

32271

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3716

7432

11148

14864

18580

<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:

0.0924

AC:

13336

AN:

144292

Hom.:

665

Cov.:

AF XY:

0.0923

AC XY:

6435

AN XY:

69710

show subpopulations

African (AFR)

AF:

0.119

AC:

4648

AN:

39048

American (AMR)

AF:

0.0583

AC:

851

AN:

14588

Ashkenazi Jewish (ASJ)

AF:

0.0964

AC:

330

AN:

3422

East Asian (EAS)

AF:

0.0687

AC:

339

AN:

4932

South Asian (SAS)

AF:

0.0553

AC:

250

AN:

4522

European-Finnish (FIN)

AF:

0.0972

AC:

800

AN:

8230

Middle Eastern (MID)

AF:

0.0755

AC:

AN:

278

European-Non Finnish (NFE)

AF:

0.0856

AC:

5679

AN:

66380

Other (OTH)

AF:

0.0853

AC:

170

AN:

1992

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

541

1082

1622

2163

2704

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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

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

Publications

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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