16-80610060-G-A

Variant names:

• chr16-80610060-G-A
• rs4613079
• NM_152342.4:c.1219-1825C>T

Variant summary

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

The NM_152342.4(CDYL2):​c.1219-1825C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 152,130 control chromosomes in the GnomAD database, including 452 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 0.045 (452 hom., cov: 32)
• Consequence: CDYL2 NM_152342.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 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.1219-1825C>T		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.1219-1825C>T		intron	N/A	ENSP00000476295.1
	CDYL2	ENST00000562812.5	TSL:5	c.1222-1825C>T		intron	N/A	ENSP00000454546.1
	CDYL2	ENST00000563890.5	TSL:5	c.1222-1825C>T		intron	N/A	ENSP00000455111.1

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6862 AN: 152012 Hom.: 448 Cov.: 32

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.0365

Gnomad FIN AF: 0.0116

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00707

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0452 AC: 6874 AN: 152130 Hom.: 452 Cov.: 32 AF XY: 0.0482 AC XY: 3582 AN XY: 74354

African (AFR) AF: 0.0538 AC: 2233 AN: 41492

American (AMR) AF: 0.163 AC: 2487 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1182 AN: 5160

South Asian (SAS) AF: 0.0363 AC: 175 AN: 4824

European-Finnish (FIN) AF: 0.0116 AC: 123 AN: 10596

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00707 AC: 481 AN: 67998

Other (OTH) AF: 0.0582 AC: 123 AN: 2112

Alfa AF: 0.0454 Hom.: 122

Bravo AF: 0.0604

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.57
PhyloP100		0.15
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: rs4613079; hg19: chr16-80643957;