rs3936503

Variant names:

• chr10-35260329-G-A
• rs3936503
• ENST00000374706.5:c.-9+9703G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-35260329-G-A
• chr10-35260329-G-C

Variant summary

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

The ENST00000374706.5(CCNY):​c.-9+9703G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,986 control chromosomes in the GnomAD database, including 10,651 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 0.37 (10651 hom., cov: 31)
• Consequence: CCNY ENST00000374706.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 22 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]

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCNY	NM_181698.4	c.-9+9703G>A		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+9703G>A		intron_variant	Intron 3 of 11	1		ENSP00000363838.1
CCNY	ENST00000493157.6	c.-224+9703G>A		intron_variant	Intron 3 of 9	5		ENSP00000473625.1
CCNY	ENST00000490012.6	c.-325+9703G>A		intron_variant	Intron 3 of 9	3		ENSP00000473487.1

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55465 AN: 151868 Hom.: 10633 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.365 AC: 55537 AN: 151986 Hom.: 10651 Cov.: 31 AF XY: 0.365 AC XY: 27091 AN XY: 74282

African (AFR) AF: 0.486 AC: 20121 AN: 41442

American (AMR) AF: 0.303 AC: 4623 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1418 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1654 AN: 5168

South Asian (SAS) AF: 0.325 AC: 1566 AN: 4816

European-Finnish (FIN) AF: 0.352 AC: 3711 AN: 10552

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21387 AN: 67966

Other (OTH) AF: 0.364 AC: 767 AN: 2110

Alfa AF: 0.334 Hom.: 28715

Bravo AF: 0.367

Asia WGS AF: 0.351 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.58
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3936503; hg19: chr10-35549257;