NM_004824.4:c.1332+29_1332+31delAAA

Variant names:

• chr6-4943770-TAAA-T
• rs34649909
• NM_004824.4:c.1332+29_1332+31delAAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378
• Publications: 0 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004824.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL	NM_004824.4	MANE Select	c.1332+29_1332+31delAAA		intron	N/A	NP_004815.3
	CDYL	NM_001368125.1		c.1494+29_1494+31delAAA		intron	N/A	NP_001355054.1
	CDYL	NM_001368126.1		c.1266+29_1266+31delAAA		intron	N/A	NP_001355055.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL	ENST00000397588.8	TSL:1 MANE Select	c.1332+29_1332+31delAAA		intron	N/A	ENSP00000380718.3
	CDYL	ENST00000328908.9	TSL:1	c.1494+29_1494+31delAAA		intron	N/A	ENSP00000330512.5
	CDYL	ENST00000343762.5	TSL:1	c.936+29_936+31delAAA		intron	N/A	ENSP00000340908.5

Frequencies

GnomAD3 genomes AF: 0.00580 AC: 837 AN: 144314 Hom.: 7 Cov.: 0

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.: 6 AF XY: 0.00234 AC XY: 1207 AN XY: 514932

African (AFR) AF: 0.0200 AC: 491 AN: 24600

American (AMR) AF: 0.00300 AC: 78 AN: 25982

Ashkenazi Jewish (ASJ) AF: 0.000108 AC: 2 AN: 18558

East Asian (EAS) AF: 0.0000580 AC: 2 AN: 34490

South Asian (SAS) AF: 0.00148 AC: 89 AN: 59948

European-Finnish (FIN) AF: 0.000437 AC: 18 AN: 41222

Middle Eastern (MID) AF: 0.00912 AC: 27 AN: 2960

European-Non Finnish (NFE) AF: 0.00211 AC: 1639 AN: 776658

Other (OTH) AF: 0.00352 AC: 155 AN: 44046

GnomAD4 genome AF: 0.00578 AC: 835 AN: 144346 Hom.: 7 Cov.: 0 AF XY: 0.00543 AC XY: 379 AN XY: 69742

African (AFR) AF: 0.0166 AC: 648 AN: 39080

American (AMR) AF: 0.00445 AC: 65 AN: 14592

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3422

East Asian (EAS) AF: 0.00 AC: 0 AN: 4932

South Asian (SAS) AF: 0.00155 AC: 7 AN: 4526

European-Finnish (FIN) AF: 0.000121 AC: 1 AN: 8232

Middle Eastern (MID) AF: 0.0107 AC: 3 AN: 280

European-Non Finnish (NFE) AF: 0.00148 AC: 98 AN: 66392

Other (OTH) AF: 0.00653 AC: 13 AN: 1990

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs34649909; hg19: chr6-4944004;