rs10764048

Positions:

• chr10-35568072-A-G

Variant summary

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

The NM_145012.6(CCNY):​c.910-982A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,038 control chromosomes in the GnomAD database, including 13,734 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 0.41 (13734 hom., cov: 33)
• Consequence: CCNY NM_145012.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCNY	NM_145012.6	c.910-982A>G		intron_variant		ENST00000374704.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNY	ENST00000374704.8	c.910-982A>G		intron_variant		1	NM_145012.6	P1
CCNY	ENST00000265375.13	c.748-982A>G		intron_variant		1
CCNY	ENST00000339497.7	c.835-982A>G		intron_variant		1
CCNY	ENST00000374706.5	c.748-982A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61762 AN: 151920 Hom.: 13693 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.407 AC: 61866 AN: 152038 Hom.: 13734 Cov.: 33 AF XY: 0.402 AC XY: 29905 AN XY: 74318

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.427

Alfa AF: 0.378 Hom.: 1427

Bravo AF: 0.428

Asia WGS AF: 0.397 AC: 1381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs10764048; hg19: chr10-35857000;