Genetic Variant ENST00000392929.6:n.426+51431C>G (chr2-134816089-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000392929.6(CCNT2-AS1):n.426+51431C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,124 control chromosomes in the GnomAD database, including 12,518 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 0.39 ( 12518 hom., cov: 32)

Consequence

CCNT2-AS1
ENST00000392929.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

6 publications found

Variant links:

Genes affected

CCNT2-AS1 (HGNC:40130): (CCNT2 antisense RNA 1)

CCNT2-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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CCNT2-AS1	ENST00000392929.6 link	n.426+51431C>G	intron_variant	Intron 3 of 3	4
CCNT2-AS1	ENST00000668300.1 link	n.149-4810C>G	intron_variant	Intron 1 of 2
CCNT2-AS1	ENST00000747809.1 link	n.165+61431C>G	intron_variant	Intron 2 of 3
CCNT2-AS1	ENST00000747810.1 link	n.169-4810C>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58613

AN:

152006

Hom.:

12513

Cov.:

show subpopulations

Gnomad AFR

AF:

0.527

Gnomad AMI

AF:

0.246

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.558

Gnomad EAS

AF:

0.378

Gnomad SAS

AF:

0.443

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.611

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.446

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

GnomAD4 genome

AF:

0.386

AC:

58659

AN:

152124

Hom.:

12518

Cov.:

AF XY:

0.386

AC XY:

28710

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.527

AC:

21848

AN:

41476

American (AMR)

AF:

0.414

AC:

6324

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.558

AC:

1937

AN:

3470

East Asian (EAS)

AF:

0.378

AC:

1954

AN:

5174

South Asian (SAS)

AF:

0.443

AC:

2138

AN:

4824

European-Finnish (FIN)

AF:

0.214

AC:

2267

AN:

10584

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.306

AC:

20840

AN:

67996

Other (OTH)

AF:

0.447

AC:

943

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1789

3577

5366

7154

8943

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

540

1080

1620

2160

2700

<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:

0.186

Hom.:

357

Bravo

AF:

0.405

Asia WGS

AF:

0.367

AC:

1276

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.50

(source)

DANN

Benign

0.70

PhyloP100

-1.3

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