rs7902346

Positions:

• chr10-35494128-G-A
• chr10-35494128-G-T

Variant summary

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

The NM_145012.6(CCNY):​c.230-7373G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,372 control chromosomes in the GnomAD database, including 10,326 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 0.36 (10326 hom., cov: 30)
• Consequence: CCNY NM_145012.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCNY	NM_145012.6	c.230-7373G>A		intron_variant		ENST00000374704.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCNY	ENST00000374704.8	c.230-7373G>A		intron_variant		1	NM_145012.6	P1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54440 AN: 151254 Hom.: 10295 Cov.: 30

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.360 AC: 54528 AN: 151372 Hom.: 10326 Cov.: 30 AF XY: 0.359 AC XY: 26533 AN XY: 73918

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.371

Alfa AF: 0.296 Hom.: 3934

Bravo AF: 0.375

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.59
DANN	Benign	0.14

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: rs7902346; hg19: chr10-35783056;