rs17761499

Positions:

• chr16-80784779-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152342.4(CDYL2):​c.24+19371A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,120 control chromosomes in the GnomAD database, including 3,010 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 0.17 (3010 hom., cov: 32)
• Consequence: CDYL2 NM_152342.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDYL2	NM_152342.4	c.24+19371A>G		intron_variant		ENST00000570137.7
CDYL2	XM_011522866.2	c.126+20124A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDYL2	ENST00000570137.7	c.24+19371A>G		intron_variant		1	NM_152342.4	P4
CDYL2	ENST00000562812.5	c.24+19371A>G		intron_variant		5		A1
CDYL2	ENST00000563890.5	c.24+19371A>G		intron_variant		5		A1
CDYL2	ENST00000566173.3	c.24+19371A>G		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26232 AN: 152002 Hom.: 3010 Cov.: 32

Gnomad AFR AF: 0.0487

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.172 AC: 26230 AN: 152120 Hom.: 3010 Cov.: 32 AF XY: 0.166 AC XY: 12353 AN XY: 74366

Gnomad4 AFR AF: 0.0486

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0973

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.198

Alfa AF: 0.232 Hom.: 3284

Bravo AF: 0.169

Asia WGS AF: 0.0430 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.78

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: rs17761499; hg19: chr16-80818676;