Genetic Variant CCNY-AS1:n.339-8216T>C (chr10-35246767-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000715770.1(CCNY-AS1):n.339-8216T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,076 control chromosomes in the GnomAD database, including 8,031 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 0.32 ( 8031 hom., cov: 32)

Consequence

CCNY-AS1
ENST00000715770.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0390

Publications

45 publications found

Variant links:

Genes affected

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

CCNY-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
CCNY-AS1	ENST00000715770.1 link	n.339-8216T>C	intron_variant	Intron 2 of 3
CCNY-AS1	ENST00000811022.1 link	n.190-8216T>C	intron_variant	Intron 1 of 2
CCNY-AS1	ENST00000811023.1 link	n.174-8216T>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.323

AC:

49014

AN:

151958

Hom.:

8017

Cov.:

show subpopulations

Gnomad AFR

AF:

0.335

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.407

Gnomad EAS

AF:

0.298

Gnomad SAS

AF:

0.325

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.334

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

GnomAD4 genome

AF:

0.323

AC:

49066

AN:

152076

Hom.:

8031

Cov.:

AF XY:

0.324

AC XY:

24078

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.335

AC:

13880

AN:

41486

American (AMR)

AF:

0.286

AC:

4368

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.407

AC:

1411

AN:

3468

East Asian (EAS)

AF:

0.298

AC:

1542

AN:

5172

South Asian (SAS)

AF:

0.326

AC:

1574

AN:

4828

European-Finnish (FIN)

AF:

0.353

AC:

3729

AN:

10572

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.317

AC:

21553

AN:

67962

Other (OTH)

AF:

0.342

AC:

721

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1723

3446

5169

6892

8615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

494

988

1482

1976

2470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.321

Hom.:

29650

Bravo

AF:

0.317

Asia WGS

AF:

0.344

AC:

1193

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.14

(source)

DANN

Benign

0.78

PhyloP100

-0.039

PromoterAI

-0.0073

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over