16-80621986-T-G

Position:

• chr16-80621986-T-G

Variant summary

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

The NM_152342.4(CDYL2):​c.835-1051A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,980 control chromosomes in the GnomAD database, including 16,504 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 0.43 (16504 hom., cov: 32)
• Consequence: CDYL2 NM_152342.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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 = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDYL2	NM_152342.4	c.835-1051A>C		intron_variant		ENST00000570137.7
CDYL2	XM_011522866.2	c.937-1051A>C		intron_variant
CDYL2	XM_011522867.3	c.826-1051A>C		intron_variant
CDYL2	XM_024450151.2	c.658-1051A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDYL2	ENST00000570137.7	c.835-1051A>C		intron_variant		1	NM_152342.4	P4

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64758 AN: 151862 Hom.: 16475 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.427 AC: 64850 AN: 151980 Hom.: 16504 Cov.: 32 AF XY: 0.431 AC XY: 31992 AN XY: 74306

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.419

Alfa AF: 0.328 Hom.: 6341

Bravo AF: 0.453

Asia WGS AF: 0.365 AC: 1272 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	0.35
DANN	Benign	0.67

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: rs12448290; hg19: chr16-80655883;