rs41472047

Variant names:

• chr16-80711878-G-A
• rs41472047
• NM_152342.4:c.25-26749C>T

Variant summary

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

The NM_152342.4(CDYL2):​c.25-26749C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 151,872 control chromosomes in the GnomAD database, including 120 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 0.033 (120 hom., cov: 31)
• Consequence: CDYL2 NM_152342.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDYL2	NM_152342.4	c.25-26749C>T		intron_variant	Intron 1 of 6	ENST00000570137.7	NP_689555.2
CDYL2	XM_011522866.2	c.127-26749C>T		intron_variant	Intron 1 of 6		XP_011521168.1
CDYL2	XM_011522867.3	c.15+24114C>T		intron_variant	Intron 1 of 6		XP_011521169.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDYL2	ENST00000570137.7	c.25-26749C>T		intron_variant	Intron 1 of 6	1	NM_152342.4	ENSP00000476295.1

Frequencies

GnomAD3 genomes AF: 0.0327 AC: 4958 AN: 151756 Hom.: 119 Cov.: 31

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0163

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0189

Gnomad FIN AF: 0.00541

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0189

Gnomad OTH AF: 0.0283

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

GnomAD4 genome AF: 0.0327 AC: 4960 AN: 151872 Hom.: 120 Cov.: 31 AF XY: 0.0309 AC XY: 2296 AN XY: 74232

Gnomad4 AFR AF: 0.0739

Gnomad4 AMR AF: 0.0161

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0189

Gnomad4 FIN AF: 0.00541

Gnomad4 NFE AF: 0.0189

Gnomad4 OTH AF: 0.0280

Alfa AF: 0.0280 Hom.: 11

Bravo AF: 0.0361

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.55

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: rs41472047; hg19: chr16-80745775;