NM_152342.4:c.835-1051A>C

Variant names:

• chr16-80621986-T-G
• rs12448290
• NM_152342.4:c.835-1051A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152342.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL2	NM_152342.4	MANE Select	c.835-1051A>C		intron	N/A	NP_689555.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL2	ENST00000570137.7	TSL:1 MANE Select	c.835-1051A>C		intron	N/A	ENSP00000476295.1
	CDYL2	ENST00000562812.5	TSL:5	c.838-1051A>C		intron	N/A	ENSP00000454546.1
	CDYL2	ENST00000563890.5	TSL:5	c.838-1051A>C		intron	N/A	ENSP00000455111.1

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

African (AFR) AF: 0.716 AC: 29662 AN: 41434

American (AMR) AF: 0.468 AC: 7155 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1772 AN: 5146

South Asian (SAS) AF: 0.305 AC: 1472 AN: 4820

European-Finnish (FIN) AF: 0.306 AC: 3236 AN: 10570

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19040 AN: 67938

Other (OTH) AF: 0.419 AC: 886 AN: 2114

Alfa AF: 0.327 Hom.: 10150

Bravo AF: 0.453

Asia WGS AF: 0.365 AC: 1272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.67
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12448290; hg19: chr16-80655883;