rs7902346

Variant names:

• chr10-35494128-G-A
• rs7902346
• NM_145012.6:c.230-7373G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-35494128-G-A
• chr10-35494128-G-T

Variant summary

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

The NM_145012.6(CCNY):​c.230-7373G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,372 control chromosomes in the GnomAD database, including 10,326 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 0.36 (10326 hom., cov: 30)
• Consequence: CCNY NM_145012.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 7 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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.230-7373G>A		intron	N/A	NP_659449.3
	CCNY	NM_001282852.2		c.155-7373G>A		intron	N/A	NP_001269781.1
	CCNY	NM_001282853.2		c.68-7373G>A		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.230-7373G>A		intron	N/A	ENSP00000363836.4
	CCNY	ENST00000339497.7	TSL:1	c.155-7373G>A		intron	N/A	ENSP00000344275.5
	CCNY	ENST00000265375.13	TSL:1	c.68-7373G>A		intron	N/A	ENSP00000265375.9

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54440 AN: 151254 Hom.: 10295 Cov.: 30

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.360 AC: 54528 AN: 151372 Hom.: 10326 Cov.: 30 AF XY: 0.359 AC XY: 26533 AN XY: 73918

African (AFR) AF: 0.473 AC: 19497 AN: 41260

American (AMR) AF: 0.373 AC: 5671 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1377 AN: 3464

East Asian (EAS) AF: 0.407 AC: 2080 AN: 5112

South Asian (SAS) AF: 0.302 AC: 1445 AN: 4784

European-Finnish (FIN) AF: 0.275 AC: 2871 AN: 10422

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20416 AN: 67814

Other (OTH) AF: 0.371 AC: 780 AN: 2104

Alfa AF: 0.303 Hom.: 5492

Bravo AF: 0.375

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.59
DANN	Benign	0.14
PhyloP100		-1.1
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: rs7902346; hg19: chr10-35783056;