rs12765826

Variant names:

• chr10-42422803-G-T
• rs12765826
• ENST00000472090.6:n.644-1874C>A

Variant summary

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

The ENST00000637719.1(CCNYL2):​n.956-1874C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,936 control chromosomes in the GnomAD database, including 8,778 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 0.33 (8778 hom., cov: 32)
• Consequence: CCNYL2 ENST00000637719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 2 publications found

Genes affected

CCNYL2 (HGNC:23495): (cyclin Y like 2 (pseudogene)) Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Predicted to be involved in positive regulation of cyclin-dependent protein serine/threonine kinase activity. Predicted to be active in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

CCNYL2 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637719.1. 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
	CCNYL2	NR_103829.1		n.956-1874C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNYL2	ENST00000472090.6	TSL:6	n.644-1874C>A		intron	N/A
	CCNYL2	ENST00000637719.1	TSL:2	n.956-1874C>A		intron	N/A
	CCNYL2	ENST00000790600.1		n.728+10451C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49786 AN: 151816 Hom.: 8775 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.328 AC: 49796 AN: 151936 Hom.: 8778 Cov.: 32 AF XY: 0.327 AC XY: 24261 AN XY: 74270

African (AFR) AF: 0.197 AC: 8146 AN: 41438

American (AMR) AF: 0.435 AC: 6643 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1181 AN: 3466

East Asian (EAS) AF: 0.325 AC: 1668 AN: 5134

South Asian (SAS) AF: 0.219 AC: 1054 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3565 AN: 10550

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26406 AN: 67950

Other (OTH) AF: 0.330 AC: 697 AN: 2112

Alfa AF: 0.347 Hom.: 1236

Bravo AF: 0.335

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.0
DANN	Benign	0.41
PhyloP100		0.028

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12765826;

hg19: chr10-42918251;