rs10764048

Variant names:

• chr10-35568072-A-G
• rs10764048
• NM_145012.6:c.910-982A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145012.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNY	NM_145012.6	MANE Select	c.910-982A>G		intron	N/A	NP_659449.3
	CCNY	NM_001282852.2		c.835-982A>G		intron	N/A	NP_001269781.1
	CCNY	NM_001282853.2		c.748-982A>G		intron	N/A	NP_001269782.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNY	ENST00000374704.8	TSL:1 MANE Select	c.910-982A>G		intron	N/A	ENSP00000363836.4
	CCNY	ENST00000339497.7	TSL:1	c.835-982A>G		intron	N/A	ENSP00000344275.5
	CCNY	ENST00000265375.13	TSL:1	c.748-982A>G		intron	N/A	ENSP00000265375.9

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

African (AFR) AF: 0.589 AC: 24442 AN: 41466

American (AMR) AF: 0.403 AC: 6165 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3466

East Asian (EAS) AF: 0.402 AC: 2071 AN: 5156

South Asian (SAS) AF: 0.328 AC: 1582 AN: 4822

European-Finnish (FIN) AF: 0.286 AC: 3027 AN: 10578

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21996 AN: 67952

Other (OTH) AF: 0.427 AC: 900 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10764048; hg19: chr10-35857000;