16-80787668-G-T

Variant names:

• chr16-80787668-G-T
• rs7204972
• NM_152342.4:c.24+16482C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152342.4(CDYL2):​c.24+16482C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 151,844 control chromosomes in the GnomAD database, including 1,161 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 0.12 (1161 hom., cov: 32)
• Consequence: CDYL2 NM_152342.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDYL2	NM_152342.4	c.24+16482C>A		intron_variant	Intron 1 of 6	ENST00000570137.7	NP_689555.2
CDYL2	XM_011522866.2	c.126+17235C>A		intron_variant	Intron 1 of 6		XP_011521168.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDYL2	ENST00000570137.7	c.24+16482C>A		intron_variant	Intron 1 of 6	1	NM_152342.4	ENSP00000476295.1
CDYL2	ENST00000562812.5	c.24+16482C>A		intron_variant	Intron 1 of 7	5		ENSP00000454546.1
CDYL2	ENST00000563890.5	c.24+16482C>A		intron_variant	Intron 1 of 7	5		ENSP00000455111.1
CDYL2	ENST00000566173.3	c.24+16482C>A		intron_variant	Intron 1 of 7	5		ENSP00000456934.1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18634 AN: 151726 Hom.: 1158 Cov.: 32

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.123 AC: 18648 AN: 151844 Hom.: 1161 Cov.: 32 AF XY: 0.122 AC XY: 9044 AN XY: 74196

African (AFR) AF: 0.0926 AC: 3835 AN: 41394

American (AMR) AF: 0.102 AC: 1552 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3466

East Asian (EAS) AF: 0.0872 AC: 451 AN: 5174

South Asian (SAS) AF: 0.226 AC: 1083 AN: 4800

European-Finnish (FIN) AF: 0.103 AC: 1079 AN: 10522

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9573 AN: 67920

Other (OTH) AF: 0.128 AC: 271 AN: 2110

Alfa AF: 0.134 Hom.: 2935

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.42
PhyloP100		0.33
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: rs7204972; hg19: chr16-80821565;