rs12765826

Positions:

• chr10-42422803-G-T

Variant summary

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

The NR_103829.1(CCNYL2):​n.956-1874C>A variant causes a intron, non coding transcript 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 NR_103829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCNYL2	NR_103829.1	n.956-1874C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNYL2	ENST00000472090.6	n.644-1874C>A		intron_variant, non_coding_transcript_variant
CCNYL2	ENST00000637719.1	n.956-1874C>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.330

Alfa AF: 0.354 Hom.: 1224

Bravo AF: 0.335

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12765826; hg19: chr10-42918251;