ENST00000605875.1:c.-108T>C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000605875.1(CCDC12):​c.-108T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 194,522 control chromosomes in the GnomAD database, including 88,897 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.94 ( 68146 hom., cov: 34)
Exomes 𝑓: 0.99 ( 20751 hom. )

Consequence

CCDC12
ENST00000605875.1 5_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.397
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 3-46979533-A-G is Benign according to our data. Variant chr3-46979533-A-G is described in ClinVar as [Benign]. Clinvar id is 1251507.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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 rank MANE Protein UniProt
CCDC12NM_144716.6 linkc.-73+2399T>C intron_variant Intron 1 of 7 NP_653317.2 J3KR35

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC12ENST00000605875.1 linkc.-108T>C 5_prime_UTR_variant Exon 1 of 4 5 ENSP00000473887.2 S4R331
CCDC12ENST00000292314.6 linkc.-73+2399T>C intron_variant Intron 1 of 7 5 ENSP00000292314.2 J3KR35
CCDC12ENST00000425441.5 linkc.-215+2399T>C intron_variant Intron 1 of 8 5 ENSP00000416263.2 Q8WUD4

Frequencies

GnomAD3 genomes
AF:
0.942
AC:
143290
AN:
152134
Hom.:
68102
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.799
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.980
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:
0.952
GnomAD4 exome
AF:
0.990
AC:
41858
AN:
42270
Hom.:
20751
Cov.:
0
AF XY:
0.991
AC XY:
21359
AN XY:
21548
show subpopulations
Gnomad4 AFR exome
AF:
0.808
Gnomad4 AMR exome
AF:
0.980
Gnomad4 ASJ exome
AF:
0.995
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
1.00
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
0.999
Gnomad4 OTH exome
AF:
0.979
GnomAD4 genome
AF:
0.942
AC:
143394
AN:
152252
Hom.:
68146
Cov.:
34
AF XY:
0.944
AC XY:
70286
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.799
Gnomad4 AMR
AF:
0.980
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:
0.953
Alfa
AF:
0.974
Hom.:
3981
Bravo
AF:
0.937

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Jun 19, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.4
DANN
Benign
0.58

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.

Other links and lift over

dbSNP: rs13062516; hg19: chr3-47021023; API