chr10-35265126-T-G

Variant names:

• chr10-35265126-T-G
• rs12261843
• ENST00000374706.5:c.-9+14500T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181698.4(CCNY):​c.-9+14500T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,980 control chromosomes in the GnomAD database, including 9,916 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 0.35 (9916 hom., cov: 32)
• Consequence: CCNY NM_181698.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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]

CCNY-AS1 (HGNC:55252): (CCNY antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCNY	NM_181698.4	c.-9+14500T>G		intron_variant	Intron 3 of 11		NP_859049.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCNY	ENST00000374706.5	c.-9+14500T>G		intron_variant	Intron 3 of 11	1		ENSP00000363838.1
CCNY	ENST00000493157.6	c.-224+14500T>G		intron_variant	Intron 3 of 9	5		ENSP00000473625.1
CCNY	ENST00000490012.6	c.-325+14500T>G		intron_variant	Intron 3 of 9	3		ENSP00000473487.1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52969 AN: 151860 Hom.: 9896 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.349 AC: 53046 AN: 151980 Hom.: 9916 Cov.: 32 AF XY: 0.350 AC XY: 25968 AN XY: 74300

African (AFR) AF: 0.496 AC: 20556 AN: 41432

American (AMR) AF: 0.286 AC: 4370 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1646 AN: 5162

South Asian (SAS) AF: 0.317 AC: 1528 AN: 4824

European-Finnish (FIN) AF: 0.333 AC: 3519 AN: 10556

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19175 AN: 67968

Other (OTH) AF: 0.342 AC: 723 AN: 2112

Alfa AF: 0.304 Hom.: 18035

Bravo AF: 0.352

Asia WGS AF: 0.349 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.9
DANN	Benign	0.79
PhyloP100		0.055
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Other links and lift over

dbSNP: rs12261843; hg19: chr10-35554054;