NM_152342.4:c.1007+3855T>C

Variant names:

• chr16-80616908-A-G
• rs13329835
• NM_152342.4:c.1007+3855T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152342.4(CDYL2):​c.1007+3855T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,116 control chromosomes in the GnomAD database, including 11,979 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (11979 hom., cov: 32)
• Consequence: CDYL2 NM_152342.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 74 publications found

Genes affected

CDYL2 (HGNC:23030): (chromodomain Y like 2) Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152342.4. 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
	CDYL2	NM_152342.4	MANE Select	c.1007+3855T>C		intron	N/A	NP_689555.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL2	ENST00000570137.7	TSL:1 MANE Select	c.1007+3855T>C		intron	N/A	ENSP00000476295.1
	CDYL2	ENST00000562812.5	TSL:5	c.1010+3855T>C		intron	N/A	ENSP00000454546.1
	CDYL2	ENST00000563890.5	TSL:5	c.1010+3855T>C		intron	N/A	ENSP00000455111.1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51836 AN: 151998 Hom.: 11951 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.0497

Gnomad SAS AF: 0.0967

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.317

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.341 AC: 51907 AN: 152116 Hom.: 11979 Cov.: 32 AF XY: 0.341 AC XY: 25357 AN XY: 74356

African (AFR) AF: 0.663 AC: 27489 AN: 41484

American (AMR) AF: 0.227 AC: 3477 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 896 AN: 3472

East Asian (EAS) AF: 0.0494 AC: 256 AN: 5178

South Asian (SAS) AF: 0.0968 AC: 467 AN: 4824

European-Finnish (FIN) AF: 0.291 AC: 3073 AN: 10572

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15231 AN: 67994

Other (OTH) AF: 0.313 AC: 659 AN: 2104

Alfa AF: 0.263 Hom.: 17856

Bravo AF: 0.353

Asia WGS AF: 0.108 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.34
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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: rs13329835; hg19: chr16-80650805;