6-4943770-TAAAAAAAA-TAAAAAAAAAAAAAAAA

Variant names:

• chr6-4943770-T-TAAAAAAAA
• rs34649909
• NM_004824.4:c.1332+24_1332+31dupAAAAAAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_004824.4(CDYL):​c.1332+24_1332+31dupAAAAAAAA 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 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000019 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Uncertain_significance. The variant received 0 ACMG points.

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+24_1332+31dupAAAAAAAA		intron	N/A	NP_004815.3
	CDYL	NM_001368125.1		c.1494+24_1494+31dupAAAAAAAA		intron	N/A	NP_001355054.1	Q9Y232-1
	CDYL	NM_001368126.1		c.1266+24_1266+31dupAAAAAAAA		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+24_1332+31dupAAAAAAAA		intron	N/A	ENSP00000380718.3	Q9Y232-2
	CDYL	ENST00000328908.9	TSL:1	c.1494+24_1494+31dupAAAAAAAA		intron	N/A	ENSP00000330512.5	Q9Y232-1
	CDYL	ENST00000343762.5	TSL:1	c.936+24_936+31dupAAAAAAAA		intron	N/A	ENSP00000340908.5	Q9Y232-4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 144312 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000194 AC: 2 AN: 1029128 Hom.: 0 Cov.: 17 AF XY: 0.00000194 AC XY: 1 AN XY: 515286

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

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: 0.00 AC: 0 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: 0.00000257 AC: 2 AN: 777116

Other (OTH) AF: 0.00 AC: 0 AN: 44076

⚠️ 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.

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 144312 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 69688

African (AFR) AF: 0.00 AC: 0 AN: 39002

American (AMR) AF: 0.00 AC: 0 AN: 14578

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 4950

South Asian (SAS) AF: 0.00 AC: 0 AN: 4544

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8232

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 304

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 66400

Other (OTH) AF: 0.00 AC: 0 AN: 1980

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;