6-4943770-TAAAAAAAA-TAA

Variant names:

• chr6-4943770-TAAAAAA-T
• rs34649909
• NM_004824.4:c.1332+26_1332+31delAAAAAA

Variant summary

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

The NM_004824.4(CDYL):​c.1332+26_1332+31delAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000583 in 1,029,136 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000058 (0 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 6 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL	NM_004824.4	MANE Select	c.1332+26_1332+31delAAAAAA		intron	N/A	NP_004815.3
	CDYL	NM_001368125.1		c.1494+26_1494+31delAAAAAA		intron	N/A	NP_001355054.1	Q9Y232-1
	CDYL	NM_001368126.1		c.1266+26_1266+31delAAAAAA		intron	N/A	NP_001355055.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL	ENST00000397588.8	TSL:1 MANE Select	c.1332+26_1332+31delAAAAAA		intron	N/A	ENSP00000380718.3	Q9Y232-2
	CDYL	ENST00000328908.9	TSL:1	c.1494+26_1494+31delAAAAAA		intron	N/A	ENSP00000330512.5	Q9Y232-1
	CDYL	ENST00000343762.5	TSL:1	c.936+26_936+31delAAAAAA		intron	N/A	ENSP00000340908.5	Q9Y232-4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000583 AC: 6 AN: 1029136 Hom.: 0 AF XY: 0.00000776 AC XY: 4 AN XY: 515290

African (AFR) AF: 0.00 AC: 0 AN: 24622

American (AMR) AF: 0.00 AC: 0 AN: 25994

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18564

East Asian (EAS) AF: 0.00 AC: 0 AN: 34504

South Asian (SAS) AF: 0.0000167 AC: 1 AN: 60032

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41260

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2960

European-Non Finnish (NFE) AF: 0.00000515 AC: 4 AN: 777124

Other (OTH) AF: 0.0000227 AC: 1 AN: 44076

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs34649909; hg19: chr6-4944004;