10-35389922-A-G

Variant names:

• chr10-35389922-A-G
• rs11010188
• NM_145012.6:c.154+52715A>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.154+52715A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,138 control chromosomes in the GnomAD database, including 6,531 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 0.29 (6531 hom., cov: 32)
• Consequence: CCNY NM_145012.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.339 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.154+52715A>G		intron	N/A	NP_659449.3
	CCNY	NM_001282852.2		c.154+52715A>G		intron	N/A	NP_001269781.1
	CCNY	NM_001282853.2		c.-71-4894A>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.154+52715A>G		intron	N/A	ENSP00000363836.4
	CCNY	ENST00000339497.7	TSL:1	c.154+52715A>G		intron	N/A	ENSP00000344275.5
	CCNY	ENST00000265375.13	TSL:1	c.-71-4894A>G		intron	N/A	ENSP00000265375.9

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43502 AN: 152020 Hom.: 6522 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.286 AC: 43526 AN: 152138 Hom.: 6531 Cov.: 32 AF XY: 0.285 AC XY: 21195 AN XY: 74374

African (AFR) AF: 0.203 AC: 8424 AN: 41510

American (AMR) AF: 0.347 AC: 5308 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1305 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1778 AN: 5168

South Asian (SAS) AF: 0.318 AC: 1532 AN: 4824

European-Finnish (FIN) AF: 0.277 AC: 2932 AN: 10576

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21186 AN: 67978

Other (OTH) AF: 0.334 AC: 706 AN: 2116

Alfa AF: 0.304 Hom.: 887

Bravo AF: 0.292

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.2
DANN	Benign	0.66
PhyloP100		-0.017
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: rs11010188; hg19: chr10-35678850;