Genetic Variant CDYL:c.1332+29_1332+31dupAAA (chr6-4943770-T-TAAA) – 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+29_1332+31dupAAA 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 0.11 ( 961 hom., cov: 0)

Exomes 𝑓: 0.088 ( 485 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 (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDYL	NM_004824.4 link	c.1332+29_1332+31dupAAA		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+29_1332+31dupAAA		intron_variant	Intron 5 of 6	1	NM_004824.4	ENSP00000380718.3		Q9Y232-2

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

15795

AN:

144126

Hom.:

960

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.0681

Gnomad ASJ

AF:

0.0731

Gnomad EAS

AF:

0.0107

Gnomad SAS

AF:

0.0648

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.0362

Gnomad NFE

AF:

0.127

Gnomad OTH

AF:

0.0911

GnomAD2 exomes

AF:

0.0555

AC:

7870

AN:

141918

AF XY:

0.0549

show subpopulations

Gnomad AFR exome

AF:

0.0667

Gnomad AMR exome

AF:

0.0276

Gnomad ASJ exome

AF:

0.0347

Gnomad EAS exome

AF:

0.00945

Gnomad FIN exome

AF:

0.0848

Gnomad NFE exome

AF:

0.0685

Gnomad OTH exome

AF:

0.0651

GnomAD4 exome

AF:

0.0879

AC:

88714

AN:

1009768

Hom.:

485

Cov.:

AF XY:

0.0858

AC XY:

43387

AN XY:

505540

show subpopulations

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

African (AFR)

AF:

0.0829

AC:

1995

AN:

24070

American (AMR)

AF:

0.0330

AC:

846

AN:

25638

Ashkenazi Jewish (ASJ)

AF:

0.0473

AC:

864

AN:

18252

East Asian (EAS)

AF:

0.00693

AC:

238

AN:

34336

South Asian (SAS)

AF:

0.0442

AC:

2617

AN:

59216

European-Finnish (FIN)

AF:

0.0984

AC:

3954

AN:

40192

Middle Eastern (MID)

AF:

0.0367

AC:

107

AN:

2914

European-Non Finnish (NFE)

AF:

0.0980

AC:

74689

AN:

761980

Other (OTH)

AF:

0.0789

AC:

3404

AN:

43170

⚠️ 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: 0.365

Heterozygous variant carriers

4480

8959

13439

17918

22398

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2784

5568

8352

11136

13920

<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:

0.110

AC:

15810

AN:

144160

Hom.:

961

Cov.:

AF XY:

0.107

AC XY:

7481

AN XY:

69646

show subpopulations

African (AFR)

AF:

0.112

AC:

4371

AN:

39024

American (AMR)

AF:

0.0680

AC:

991

AN:

14570

Ashkenazi Jewish (ASJ)

AF:

0.0731

AC:

250

AN:

3422

East Asian (EAS)

AF:

0.0110

AC:

AN:

4930

South Asian (SAS)

AF:

0.0646

AC:

292

AN:

4518

European-Finnish (FIN)

AF:

0.136

AC:

1113

AN:

8186

Middle Eastern (MID)

AF:

0.0321

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.127

AC:

8414

AN:

66344

Other (OTH)

AF:

0.0932

AC:

185

AN:

1986

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

619

1238

1858

2477

3096

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<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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6-4943770-TAAAAAAAA-TAAAAAAAAAAA

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