rs4613079

Positions:

• chr16-80610060-G-A
• chr16-80610060-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDYL2	NM_152342.4	c.1219-1825C>T		intron_variant		ENST00000570137.7
CDYL2	XM_011522866.2	c.1321-1825C>T		intron_variant
CDYL2	XM_011522867.3	c.1210-1825C>T		intron_variant
CDYL2	XM_024450151.2	c.1042-1825C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDYL2	ENST00000570137.7	c.1219-1825C>T		intron_variant		1	NM_152342.4	P4
CDYL2	ENST00000562812.5	c.1222-1825C>T		intron_variant		5		A1
CDYL2	ENST00000563890.5	c.1222-1825C>T		intron_variant		5		A1
CDYL2	ENST00000566173.3	c.1222-1825C>T		intron_variant		5		A1

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

Gnomad4 AFR AF: 0.0538

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.0363

Gnomad4 FIN AF: 0.0116

Gnomad4 NFE AF: 0.00707

Gnomad4 OTH AF: 0.0582

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs4613079; hg19: chr16-80643957;