rs2504353

chr10-35380400-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+43193G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 152,242 control chromosomes in the GnomAD database, including 938 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 0.082 (938 hom., cov: 32)
• Consequence: CCNY NM_145012.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCNY	NM_145012.6	c.154+43193G>A		intron_variant		ENST00000374704.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNY	ENST00000374704.8	c.154+43193G>A		intron_variant		1	NM_145012.6	P1

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12409 AN: 152124 Hom.: 929 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.0691

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0329

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0818 AC: 12451 AN: 152242 Hom.: 938 Cov.: 32 AF XY: 0.0804 AC XY: 5983 AN XY: 74452

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0607

Gnomad4 ASJ AF: 0.0691

Gnomad4 EAS AF: 0.0557

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.0148

Gnomad4 NFE AF: 0.0329

Gnomad4 OTH AF: 0.0696

Alfa AF: 0.0602 Hom.: 68

Bravo AF: 0.0900

Asia WGS AF: 0.0400 AC: 140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.19
Dann	Benign	0.57

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: rs2504353; hg19: chr10-35669328;