16-80623875-C-T

Variant names:

• chr16-80623875-C-T
• rs13334600
• NM_152342.4:c.835-2940G>A

Variant summary

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

The NM_152342.4(CDYL2):​c.835-2940G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,042 control chromosomes in the GnomAD database, including 6,297 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 0.16 (6297 hom., cov: 32)
• Consequence: CDYL2 NM_152342.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDYL2	NM_152342.4	c.835-2940G>A		intron_variant	Intron 3 of 6	ENST00000570137.7	NP_689555.2
CDYL2	XM_011522866.2	c.937-2940G>A		intron_variant	Intron 3 of 6		XP_011521168.1
CDYL2	XM_011522867.3	c.826-2940G>A		intron_variant	Intron 3 of 6		XP_011521169.1
CDYL2	XM_024450151.2	c.658-2940G>A		intron_variant	Intron 3 of 6		XP_024305919.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDYL2	ENST00000570137.7	c.835-2940G>A		intron_variant	Intron 3 of 6	1	NM_152342.4	ENSP00000476295.1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24278 AN: 151924 Hom.: 6272 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0623

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00346

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.160 AC: 24350 AN: 152042 Hom.: 6297 Cov.: 32 AF XY: 0.156 AC XY: 11611 AN XY: 74350

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.0621

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.0423

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.00283

Gnomad4 NFE AF: 0.00346

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0257 Hom.: 125

Bravo AF: 0.183

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.71
DANN	Benign	0.73

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: rs13334600; hg19: chr16-80657772;