NM_152342.4:c.*1270T>C

Variant names:

• chr16-80603118-A-G
• rs8063688
• NM_152342.4:c.*1270T>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.*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
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL2	NM_152342.4	MANE Select	c.*1270T>C		3_prime_UTR	Exon 7 of 7	NP_689555.2	Q8N8U2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDYL2	ENST00000570137.7	TSL:1 MANE Select	c.*1270T>C		3_prime_UTR	Exon 7 of 7	ENSP00000476295.1	Q8N8U2
	CDYL2	ENST00000919359.1		c.*1270T>C		3_prime_UTR	Exon 6 of 6	ENSP00000589418.1

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 9 AN: 36

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.840 AC: 34810 AN: 41460

American (AMR) AF: 0.500 AC: 7637 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1697 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1774 AN: 5152

South Asian (SAS) AF: 0.289 AC: 1390 AN: 4804

European-Finnish (FIN) AF: 0.358 AC: 3779 AN: 10566

Middle Eastern (MID) AF: 0.514 AC: 149 AN: 290

European-Non Finnish (NFE) AF: 0.391 AC: 26578 AN: 67930

Other (OTH) AF: 0.515 AC: 1087 AN: 2110

Alfa AF: 0.432 Hom.: 24025

Bravo AF: 0.549

Asia WGS AF: 0.368 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		0.12
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: rs8063688; hg19: chr16-80637015;