16-80616908-A-G

Position:

• chr16-80616908-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.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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDYL2	NM_152342.4	c.1007+3855T>C		intron_variant		ENST00000570137.7	NP_689555.2
CDYL2	XM_011522866.2	c.1109+3855T>C		intron_variant			XP_011521168.1
CDYL2	XM_011522867.3	c.998+3855T>C		intron_variant			XP_011521169.1
CDYL2	XM_024450151.2	c.830+3855T>C		intron_variant			XP_024305919.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDYL2	ENST00000570137.7	c.1007+3855T>C		intron_variant		1	NM_152342.4	ENSP00000476295	P4

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

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.0494

Gnomad4 SAS AF: 0.0968

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.313

Alfa AF: 0.253 Hom.: 5263

Bravo AF: 0.353

Asia WGS AF: 0.108 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.34

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: rs13329835; hg19: chr16-80650805;