Variant chr3-46979345-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_144716.6(CCDC12):c.-72-2502T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.946 in 152,382 control chromosomes in the GnomAD database, including 68,686 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.95 ( 68624 hom., cov: 34)

Exomes 𝑓: 0.99 ( 62 hom. )

Consequence

CCDC12
NM_144716.6 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.669

Variant links:

Genes affected

CCDC12 (HGNC:28332): (coiled-coil domain containing 12) Predicted to be part of U2-type spliceosomal complex and post-mRNA release spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]

CCDC12 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 3-46979345-A-T is Benign according to our data. Variant chr3-46979345-A-T is described in ClinVar as [Benign]. Clinvar id is 1288588.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC12	NM_144716.6 linkuse as main transcript	c.-72-2502T>A		intron_variant			NP_653317.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	Appris
CCDC12	ENST00000292314.6 linkuse as main transcript	c.-72-2502T>A	intron_variant	5	ENSP00000292314
CCDC12	ENST00000425441.5 linkuse as main transcript	c.-214-2305T>A	intron_variant	5	ENSP00000416263	P1
CCDC12	ENST00000446836.5 linkuse as main transcript	c.-111-2502T>A	intron_variant	3	ENSP00000387490

Frequencies

GnomAD3 genomes

AF:

0.946

AC:

143862

AN:

152138

Hom.:

68580

Cov.:

show subpopulations

Gnomad AFR

AF:

0.812

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.981

Gnomad ASJ

AF:

0.995

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.987

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.955

GnomAD4 exome

AF:

0.992

AC:

125

AN:

126

Hom.:

AF XY:

0.988

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.900

Gnomad4 AMR exome

AF:

1.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.946

AC:

143966

AN:

152256

Hom.:

68624

Cov.:

AF XY:

0.948

AC XY:

70550

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.812

Gnomad4 AMR

AF:

0.981

Gnomad4 ASJ

AF:

0.995

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

1.00

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.955

Alfa

AF:

0.969

Hom.:

8913

Bravo

AF:

0.938

Asia WGS

AF:

0.992

AC:

3450

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.3

DANN

Benign

0.41

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over