rs2474519

Positions:

• chr10-35352643-G-A

Variant summary

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

The NM_145012.6(CCNY):​c.154+15436G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,128 control chromosomes in the GnomAD database, including 10,845 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 0.37 (10845 hom., cov: 33)
• Consequence: CCNY NM_145012.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

Genes affected

CCNY (HGNC:23354): (cyclin Y) Cyclins, such as CCNY, control cell division cycles and regulate cyclin-dependent kinases (e.g., CDC2; MIM 116940) (Li et al., 2009 [PubMed 18060517]).[supplied by OMIM, May 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCNY	NM_145012.6	c.154+15436G>A		intron_variant		ENST00000374704.8	NP_659449.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCNY	ENST00000374704.8	c.154+15436G>A		intron_variant		1	NM_145012.6	ENSP00000363836	P1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56807 AN: 152010 Hom.: 10823 Cov.: 33

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.374 AC: 56882 AN: 152128 Hom.: 10845 Cov.: 33 AF XY: 0.371 AC XY: 27580 AN XY: 74358

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.405

Alfa AF: 0.365 Hom.: 9366

Bravo AF: 0.388

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.75

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: rs2474519; hg19: chr10-35641571;