16-80613487-A-G

Position:

• chr16-80613487-A-G

Variant summary

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

The NM_152342.4(CDYL2):​c.1008-651T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,050 control chromosomes in the GnomAD database, including 4,324 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 0.23 (4324 hom., cov: 32)
• Consequence: CDYL2 NM_152342.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

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=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDYL2	NM_152342.4	c.1008-651T>C		intron_variant		ENST00000570137.7
CDYL2	XM_011522866.2	c.1110-651T>C		intron_variant
CDYL2	XM_011522867.3	c.999-651T>C		intron_variant
CDYL2	XM_024450151.2	c.831-651T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDYL2	ENST00000570137.7	c.1008-651T>C		intron_variant		1	NM_152342.4	P4

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35648 AN: 151930 Hom.: 4322 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.235 AC: 35665 AN: 152050 Hom.: 4324 Cov.: 32 AF XY: 0.241 AC XY: 17897 AN XY: 74314

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.265

Alfa AF: 0.235 Hom.: 8900

Bravo AF: 0.240

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.6
DANN	Benign	0.85

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: rs2316184; hg19: chr16-80647384;