rs2504353

Variant names:

• chr10-35380400-G-A
• rs2504353
• NM_145012.6:c.154+43193G>A

Variant summary

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

The NM_145012.6(CCNY):​c.154+43193G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 152,242 control chromosomes in the GnomAD database, including 938 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 0.082 (938 hom., cov: 32)
• Consequence: CCNY NM_145012.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNY	NM_145012.6	MANE Select	c.154+43193G>A		intron	N/A	NP_659449.3
	CCNY	NM_001282852.2		c.154+43193G>A		intron	N/A	NP_001269781.1	Q8ND76-2
	CCNY	NM_001282853.2		c.-71-14416G>A		intron	N/A	NP_001269782.1	Q8ND76-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCNY	ENST00000374704.8	TSL:1 MANE Select	c.154+43193G>A		intron	N/A	ENSP00000363836.4	Q8ND76-1
	CCNY	ENST00000339497.7	TSL:1	c.154+43193G>A		intron	N/A	ENSP00000344275.5	Q8ND76-2
	CCNY	ENST00000265375.13	TSL:1	c.-71-14416G>A		intron	N/A	ENSP00000265375.9	Q8ND76-3

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12409 AN: 152124 Hom.: 929 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0607

Gnomad ASJ AF: 0.0691

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0329

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0818 AC: 12451 AN: 152242 Hom.: 938 Cov.: 32 AF XY: 0.0804 AC XY: 5983 AN XY: 74452

African (AFR) AF: 0.200 AC: 8310 AN: 41514

American (AMR) AF: 0.0607 AC: 928 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0691 AC: 240 AN: 3472

East Asian (EAS) AF: 0.0557 AC: 289 AN: 5184

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4824

European-Finnish (FIN) AF: 0.0148 AC: 157 AN: 10606

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0329 AC: 2236 AN: 68026

Other (OTH) AF: 0.0696 AC: 147 AN: 2112

Alfa AF: 0.0657 Hom.: 87

Bravo AF: 0.0900

Asia WGS AF: 0.0400 AC: 140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.57
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2504353; hg19: chr10-35669328;