Genetic Variant CDYL:c.1332+29_1332+31delAAA (chr6-4943770-TAAA-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_004824.4(CDYL):c.1332+29_1332+31delAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00284 in 1,172,810 control chromosomes in the GnomAD database, including 13 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0058 ( 7 hom., cov: 0)

Exomes 𝑓: 0.0024 ( 6 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.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00578 (835/144346) while in subpopulation AFR AF = 0.0166 (648/39080). AF 95% confidence interval is 0.0155. There are 7 homozygotes in GnomAd4. There are 379 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High AC in GnomAd4 at 835 AD gene.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes

AF:

0.00580

AC:

837

AN:

144314

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0166

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00446

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00154

Gnomad FIN

AF:

0.000121

Gnomad MID

AF:

0.0132

Gnomad NFE

AF:

0.00149

Gnomad OTH

AF:

0.00657

GnomAD4 exome

AF:

0.00243

AC:

2501

AN:

1028464

Hom.:

AF XY:

0.00234

AC XY:

1207

AN XY:

514932

show subpopulations

African (AFR)

AF:

0.0200

AC:

491

AN:

24600

American (AMR)

AF:

0.00300

AC:

AN:

25982

Ashkenazi Jewish (ASJ)

AF:

0.000108

AC:

AN:

18558

East Asian (EAS)

AF:

0.0000580

AC:

AN:

34490

South Asian (SAS)

AF:

0.00148

AC:

AN:

59948

European-Finnish (FIN)

AF:

0.000437

AC:

AN:

41222

Middle Eastern (MID)

AF:

0.00912

AC:

AN:

2960

European-Non Finnish (NFE)

AF:

0.00211

AC:

1639

AN:

776658

Other (OTH)

AF:

0.00352

AC:

155

AN:

44046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.441

Heterozygous variant carriers

175

262

350

437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

160

240

320

400

<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:

0.00578

AC:

835

AN:

144346

Hom.:

Cov.:

AF XY:

0.00543

AC XY:

379

AN XY:

69742

show subpopulations

African (AFR)

AF:

0.0166

AC:

648

AN:

39080

American (AMR)

AF:

0.00445

AC:

AN:

14592

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3422

East Asian (EAS)

AF:

0.00

AC:

AN:

4932

South Asian (SAS)

AF:

0.00155

AC:

AN:

4526

European-Finnish (FIN)

AF:

0.000121

AC:

AN:

8232

Middle Eastern (MID)

AF:

0.0107

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.00148

AC:

AN:

66392

Other (OTH)

AF:

0.00653

AC:

AN:

1990

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.529

Heterozygous variant carriers

118

157

196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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

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

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6-4943770-TAAAAAAAA-TAAAAA

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