Genetic Variant CDYL:c.1332+28_1332+31dupAAAA (chr6-4943770-T-TAAAA) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_004824.4(CDYL):c.1332+28_1332+31dupAAAA 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 0.0018 ( 2 hom., cov: 0)

Exomes 𝑓: 0.0068 ( 0 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: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAd4 at 267 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDYL	NM_004824.4 link	c.1332+28_1332+31dupAAAA		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+28_1332+31dupAAAA		intron_variant	Intron 5 of 6	1	NM_004824.4	ENSP00000380718.3		Q9Y232-2

Frequencies

GnomAD3 genomes

AF:

0.00185

AC:

267

AN:

144302

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00428

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000549

Gnomad ASJ

AF:

0.000584

Gnomad EAS

AF:

0.000404

Gnomad SAS

AF:

0.000440

Gnomad FIN

AF:

0.000486

Gnomad MID

AF:

0.00329

Gnomad NFE

AF:

0.00119

Gnomad OTH

AF:

0.00101

GnomAD4 exome

AF:

0.00683

AC:

7001

AN:

1024850

Hom.:

Cov.:

AF XY:

0.00660

AC XY:

3387

AN XY:

513136

show subpopulations

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

African (AFR)

AF:

0.00854

AC:

209

AN:

24460

American (AMR)

AF:

0.00170

AC:

AN:

25930

Ashkenazi Jewish (ASJ)

AF:

0.00427

AC:

AN:

18512

East Asian (EAS)

AF:

0.000377

AC:

AN:

34478

South Asian (SAS)

AF:

0.00510

AC:

305

AN:

59846

European-Finnish (FIN)

AF:

0.00611

AC:

251

AN:

41088

Middle Eastern (MID)

AF:

0.00169

AC:

AN:

2956

European-Non Finnish (NFE)

AF:

0.00754

AC:

5835

AN:

773668

Other (OTH)

AF:

0.00592

AC:

260

AN:

43912

⚠️ 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: 0.299

Heterozygous variant carriers

565

1130

1695

2260

2825

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

226

452

678

904

1130

<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:

0.00185

AC:

267

AN:

144334

Hom.:

Cov.:

AF XY:

0.00179

AC XY:

125

AN XY:

69736

show subpopulations

African (AFR)

AF:

0.00427

AC:

167

AN:

39078

American (AMR)

AF:

0.000548

AC:

AN:

14588

Ashkenazi Jewish (ASJ)

AF:

0.000584

AC:

AN:

3422

East Asian (EAS)

AF:

0.000406

AC:

AN:

4932

South Asian (SAS)

AF:

0.000442

AC:

AN:

4526

European-Finnish (FIN)

AF:

0.000486

AC:

AN:

8230

Middle Eastern (MID)

AF:

0.00357

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.00119

AC:

AN:

66388

Other (OTH)

AF:

0.00101

AC:

AN:

1990

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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

(source)

Splicing

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

Publications

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6-4943770-TAAAAAAAA-TAAAAAAAAAAAA

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