rs8063688

Positions:

• chr16-80603118-A-G
• chr16-80603118-A-T

Variant summary

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

The NM_152342.4(CDYL2):​c.*1270T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,004 control chromosomes in the GnomAD database, including 23,894 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 0.52 (23894 hom., cov: 31)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: CDYL2 NM_152342.4 3_prime_UTR
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDYL2	NM_152342.4	c.*1270T>C		3_prime_UTR_variant	7/7	ENST00000570137.7	NP_689555.2
CDYL2	XM_011522866.2	c.*1270T>C		3_prime_UTR_variant	7/7		XP_011521168.1
CDYL2	XM_011522867.3	c.*1270T>C		3_prime_UTR_variant	7/7		XP_011521169.1
CDYL2	XM_024450151.2	c.*1270T>C		3_prime_UTR_variant	7/7		XP_024305919.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDYL2	ENST00000570137.7	c.*1270T>C		3_prime_UTR_variant	7/7	1	NM_152342.4	ENSP00000476295	P4

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79099 AN: 151844 Hom.: 23843 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.519

GnomAD4 exome AF: 0.250 AC: 10 AN: 40 Hom.: 0 Cov.: 0 AF XY: 0.208 AC XY: 5 AN XY: 24

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.521 AC: 79206 AN: 151964 Hom.: 23894 Cov.: 31 AF XY: 0.517 AC XY: 38398 AN XY: 74280

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.515

Alfa AF: 0.418 Hom.: 14967

Bravo AF: 0.549

Asia WGS AF: 0.368 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.56

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: rs8063688; hg19: chr16-80637015;