chr3-46979345-A-T

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

2

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]

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 UniProt
CCDC12NM_144716.6 linkuse as main transcriptc.-72-2502T>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCDC12ENST00000292314.6 linkuse as main transcriptc.-72-2502T>A intron_variant 5
CCDC12ENST00000425441.5 linkuse as main transcriptc.-214-2305T>A intron_variant 5 P1
CCDC12ENST00000446836.5 linkuse as main transcriptc.-111-2502T>A intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.946
AC:
143862
AN:
152138
Hom.:
68580
Cov.:
34
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.:
62
AF XY:
0.988
AC XY:
81
AN XY:
82
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.:
34
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 submitterclinical testingGeneDxJun 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.

Other links and lift over

dbSNP: rs13062185; hg19: chr3-47020835; API