10-12896961-C-T

Variant summary

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

The NM_031455.4(CCDC3):​c.*1455G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,258 control chromosomes in the GnomAD database, including 4,249 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 0.21 ( 4238 hom., cov: 32)
Exomes 𝑓: 0.32 ( 11 hom. )

Consequence

CCDC3
NM_031455.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00300

Publications

9 publications found
Variant links:
Genes affected
CCDC3 (HGNC:23813): (coiled-coil domain containing 3) Involved in negative regulation of gene expression; negative regulation of lipid metabolic process; and negative regulation of tumor necrosis factor-mediated signaling pathway. Located in endoplasmic reticulum and extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC3NM_031455.4 linkc.*1455G>A 3_prime_UTR_variant Exon 3 of 3 ENST00000378825.5 NP_113643.1 Q9BQI4-1
CCDC3NM_001282658.2 linkc.*1455G>A 3_prime_UTR_variant Exon 7 of 7 NP_001269587.1 Q9BQI4-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC3ENST00000378825.5 linkc.*1455G>A 3_prime_UTR_variant Exon 3 of 3 1 NM_031455.4 ENSP00000368102.3 Q9BQI4-1
CCDC3ENST00000378839.1 linkc.*1455G>A 3_prime_UTR_variant Exon 7 of 7 2 ENSP00000368116.1 Q9BQI4-2
ENSG00000285520ENST00000649832.1 linkn.511-1551C>T intron_variant Intron 2 of 4

Frequencies

GnomAD3 genomes
AF:
0.213
AC:
32362
AN:
151964
Hom.:
4242
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0625
Gnomad AMI
AF:
0.255
Gnomad AMR
AF:
0.195
Gnomad ASJ
AF:
0.374
Gnomad EAS
AF:
0.219
Gnomad SAS
AF:
0.137
Gnomad FIN
AF:
0.261
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.297
Gnomad OTH
AF:
0.225
GnomAD4 exome
AF:
0.324
AC:
57
AN:
176
Hom.:
11
Cov.:
0
AF XY:
0.319
AC XY:
46
AN XY:
144
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
4
American (AMR)
AF:
0.00
AC:
0
AN:
2
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2
European-Finnish (FIN)
AF:
0.500
AC:
1
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.346
AC:
56
AN:
162
Other (OTH)
AF:
0.00
AC:
0
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.485
Heterozygous variant carriers
0
1
3
4
6
7
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.213
AC:
32346
AN:
152082
Hom.:
4238
Cov.:
32
AF XY:
0.210
AC XY:
15587
AN XY:
74330
show subpopulations
African (AFR)
AF:
0.0624
AC:
2590
AN:
41516
American (AMR)
AF:
0.194
AC:
2969
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.374
AC:
1294
AN:
3464
East Asian (EAS)
AF:
0.220
AC:
1135
AN:
5164
South Asian (SAS)
AF:
0.136
AC:
651
AN:
4802
European-Finnish (FIN)
AF:
0.261
AC:
2763
AN:
10580
Middle Eastern (MID)
AF:
0.255
AC:
75
AN:
294
European-Non Finnish (NFE)
AF:
0.297
AC:
20168
AN:
67958
Other (OTH)
AF:
0.222
AC:
469
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
1203
2405
3608
4810
6013
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
342
684
1026
1368
1710
<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:
0.271
Hom.:
10138
Bravo
AF:
0.204
Asia WGS
AF:
0.167
AC:
584
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
6.5
DANN
Benign
0.44
PhyloP100
0.0030
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs2280076; hg19: chr10-12938961; API